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Letters in Drug Design & Discovery

Editor-in-Chief

ISSN (Print): 1570-1808
ISSN (Online): 1875-628X

Research Article

Triamcinolone as a Potential Inhibitor of SARS-CoV-2 Main Protease and Cytokine Storm: An In silico Study

Author(s): Amaresh Mishra, Faizan Abul Qais, Yamini Pathak, Ihosvany Camps and Vishwas Tripathi*

Volume 20, Issue 9, 2023

Published on: 18 August, 2022

Page: [1230 - 1242] Pages: 13

DOI: 10.2174/1570180819666220401142351

Price: $65

Abstract

Background: An ongoing global public health concern is the emerging COVID-19 pandemic triggered by acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Mpro, a main protease of SARSCoV- 2, has been established as a potential drug target because of its direct role in viral replication and ability to infiltrate the multiple host pathways.

Objective: This research aims to classify new therapeutic drug candidates who may be repositioned for COVID-19 therapeutics.

Methods: We have taken similar drug compounds of Dexamethasone and targeted the main protease of SARS-CoV-2 (Mpro) along with the key molecules involved in the 'cytokine storm.' Further, we did MD simulations and calculated the molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) on the active site of the main protease of SARS-CoV-2 (Mpro) and TNF-α, IL-6, & IL-1β to explore the binding affinity and stability.

Results: Based on our study outcome, Triamcinolone emerged as the most promising inhibitor of the main protease of SARS-CoV-2 (Mpro) and the cytokine storm molecules, i.e., TNF-α, IL-6, and IL-1β.

Conclusion: This research investigates the repositioning of COVID-19 drugs as a new therapeutic application.

Keywords: COVID-19, cytokine storm, main protease, molecular docking, MD simulation, protease inhibitor, triamcinolone.

Graphical Abstract
[1]
CDC Weekly C. The epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (COVID-19) — China. 2020.
[2]
Cucinotta, D.; Vanelli, M. WHO declares COVID-19 a pandemic. Acta Biomed., 2020, 91(1), 157-160.
[PMID: 32191675]
[3]
Yu, I.T.S.; Li, Y.; Wong, T.W.; Tam, W.; Chan, A.T.; Lee, J.H.W.; Leung, D.Y.; Ho, T. Evidence of airborne transmission of the severe acute respiratory syndrome virus. N. Engl. J. Med., 2004, 350(17), 1731-1739.
[http://dx.doi.org/10.1056/NEJMoa032867] [PMID: 15102999]
[4]
Chen, Y.; Li, L. SARS-CoV-2: Virus dynamics and host response. Lancet Infect. Dis., 2020, 20(5), 515-516.
[http://dx.doi.org/10.1016/S1473-3099(20)30235-8] [PMID: 32213336]
[5]
Hung, I.F.N.; Lung, K.C.; Tso, E.Y.K.; Liu, R.; Chung, T.W.H.; Chu, M.Y.; Ng, Y.Y.; Lo, J.; Chan, J.; Tam, A.R.; Shum, H.P.; Chan, V.; Wu, A.K.; Sin, K.M.; Leung, W.S.; Law, W.L.; Lung, D.C.; Sin, S.; Yeung, P.; Yip, C.C.; Zhang, R.R.; Fung, A.Y.; Yan, E.Y.; Leung, K.H.; Ip, J.D.; Chu, A.W.; Chan, W.M.; Ng, A.C.; Lee, R.; Fung, K.; Yeung, A.; Wu, T.C.; Chan, J.W.; Yan, W.W.; Chan, W.M.; Chan, J.F.; Lie, A.K.; Tsang, O.T.; Cheng, V.C.; Que, T.L.; Lau, C.S.; Chan, K.H.; To, K.K.; Yuen, K.Y. Triple combination of interferon beta-1b, lopinavir-ritonavir, and ribavirin in the treatment of patients admitted to hospital with COVID-19: An open-label, randomised, phase 2 trial. Lancet, 2020, 395(10238), 1695-1704.
[http://dx.doi.org/10.1016/S0140-6736(20)31042-4] [PMID: 32401715]
[6]
Viveiros Rosa, S.G.; Santos, W.C. Clinical trials on drug repositioning for COVID-19 treatment. Rev. Panam. Salud Publica, 2020.
[7]
Mahase, E. Coronavirus COVID-19 has killed more people than SARS and MERS combined, despite lower case fatality rate. BMJ, 2020, 368, m641.
[http://dx.doi.org/10.1136/bmj.m641] [PMID: 32071063]
[8]
Li, L. quan; Huang, T; qing, Wang Y; ping, Wang Z; Liang, Y; bi, Huang T COVID-19 patients’ clinical characteristics, discharge rate, and fatality rate of meta-analysis. J. Med. Virol., 2020, 92(6), 577-583.
[9]
Chen, N.; Zhou, M.; Dong, X.; Qu, J.; Gong, F.; Han, Y.; Qiu, Y.; Wang, J.; Liu, Y.; Wei, Y.; Xia, J.; Yu, T.; Zhang, X.; Zhang, L. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: A descriptive study. Lancet, 2020, 395(10223), 507-513.
[http://dx.doi.org/10.1016/S0140-6736(20)30211-7] [PMID: 32007143]
[10]
Bai, Y.; Yao, L.; Wei, T.; Tian, F.; Jin, D.Y.; Chen, L.; Wang, M. Presumed asymptomatic carrier transmission of COVID-19. JAMA, 2020, 323(14), 1406-1407.
[http://dx.doi.org/10.1001/jama.2020.2565] [PMID: 32083643]
[11]
Kouznetsova, J.; Sun, W.; Martínez-Romero, C.; Tawa, G.; Shinn, P.; Chen, C.Z.; Schimmer, A.; Sanderson, P.; McKew, J.C.; Zheng, W.; García-Sastre, A. Identification of 53 compounds that block Ebola virus-like particle entry via a repurposing screen of approved drugs. Emerg. Microbes Infect., 2014, 3(12), e84.
[http://dx.doi.org/10.1038/emi.2014.88] [PMID: 26038505]
[12]
He, S.; Lin, B.; Chu, V.; Hu, Z.; Hu, X.; Xiao, J.; Wang, A.Q.; Schweitzer, C.J.; Li, Q.; Imamura, M.; Hiraga, N.; Southall, N.; Ferrer, M.; Zheng, W.; Chayama, K.; Marugan, J.J.; Liang, T.J. Repurposing of the antihistamine chlorcyclizine and related compounds for treatment of hepatitis C virus infection. Sci. Transl. Med., 2015, 7(282), 282ra49.
[http://dx.doi.org/10.1126/scitranslmed.3010286] [PMID: 25855495]
[13]
Fan, H.H.; Wang, L.Q.; Liu, W.L.; An, X.P.; Liu, Z.D.; He, X.Q. Repurposing of clinically approved drugs for treatment of coronavirus disease 2019 in a 2019-novel coronavirus-related coronavirus model. Chin. Med. J. (Engl.), 2020, 133(9), 1051-1056.
[14]
Pathak, Y.; Mishra, A.; Choudhir, G.; Kumar, A.; Tripathi, V. Rifampicin and Letermovir as potential repurposed drug candidate for COVID-19 treatment: Insights from an in silico study. Pharmacol. Rep., 2021, 73(3), 926-938.
[http://dx.doi.org/10.1007/s43440-021-00228-0] [PMID: 33970450]
[15]
Mehta, P.; McAuley, D.F.; Brown, M.; Sanchez, E.; Tattersall, R.S.; Manson, J.J. HLH Across Speciality Collaboration. UK. COVID-19: Consider cytokine storm syndromes and immunosuppression. Lancet, 2020, 395(10229), 1033-1034.
[http://dx.doi.org/10.1016/S0140-6736(20)30628-0] [PMID: 32192578]
[16]
Costela-Ruiz, V.J.; Illescas-Montes, R.; Puerta-Puerta, J.M.; Ruiz, C.; Melguizo-Rodríguez, L. SARS-CoV-2 infection: The role of cytokines in COVID-19 disease. Cytokine Growth Factor Rev., 2020, 54, 62-75.
[http://dx.doi.org/10.1016/j.cytogfr.2020.06.001] [PMID: 32513566]
[17]
Tang, Y.; Liu, J.; Zhang, D.; Xu, Z.; Ji, J.; Wen, C. Cytokine storm in COVID-19: The current evidence and treatment strategies. Front. Immunol., 2020, 11, 1708.
[http://dx.doi.org/10.3389/fimmu.2020.01708]
[18]
Ding, Y.; Qin, L.; Kotenko, S.V.; Pestka, S.; Bromberg, J.S. A single amino acid determines the immunostimulatory activity of interleukin 10. J. Exp. Med., 2000, 191(2), 213-224.
[http://dx.doi.org/10.1084/jem.191.2.213] [PMID: 10637267]
[19]
Ding, Y.; Qin, L.; Zamarin, D.; Kotenko, S.V.; Pestka, S.; Moore, K.W.; Bromberg, J.S. Differential IL-10R1 expression plays a critical role in IL-10-mediated immune regulation. J. Immunol., 2001, 167(12), 6884-6892.
[http://dx.doi.org/10.4049/jimmunol.167.12.6884] [PMID: 11739506]
[20]
Raftery, M.J.; Wieland, D.; Gronewald, S.; Kraus, A.A.; Giese, T.; Schönrich, G. Shaping phenotype, function, and survival of dendritic cells by cytomegalovirus-encoded IL-10. J. Immunol., 2004, 173(5), 3383-3391.
[http://dx.doi.org/10.4049/jimmunol.173.5.3383] [PMID: 15322202]
[21]
Theoharides, T.C.; Conti, P. Dexamethasone for COVID-19? Not so fast. J. Biol. Regul. Homeost. Agents, 2020, 34(3), 1241-1243.
[22]
Abdolahi, N.; Kaheh, E.; Golsha, R.; Khodabakhshi, B.; Norouzi, A.; Khandashpoor, M. Letter to the editor: Efficacy of different methods of combination regimen administrations including Dexamethasone, intravenous immunoglobulin, and interferon-beta to treat critically ill COVID-19 patients: a structured summary of a study protocol for a randomized controlled trial. Trials, 2020, 21(1)
[23]
Lim, M.A.; Pranata, R. Worrying situation regarding the use of dexamethasone for COVID-19. Ther. Adv. Respir. Dis., 2020, 14, 1753466620942131.
[http://dx.doi.org/10.1177/1753466620942131] [PMID: 32684095]
[24]
Rhen, T.; Cidlowski, J.A. Antiinflammatory action of glucocorticoids--new mechanisms for old drugs. N. Engl. J. Med., 2005, 353(16), 1711-1723.
[http://dx.doi.org/10.1056/NEJMra050541] [PMID: 16236742]
[25]
Selvaraj, V.; Dapaah-Afriyie, K.; Finn, A.; Flanigan, T.P. Short-Term Dexamethasone in SARS-CoV-2 Patients. R.I. Med. J., 2020, 103(6)
[26]
Tahir Ul Qamar, M.; Alqahtani, S.M.; Alamri, M.A.; Chen, L.L. Structural basis of SARS-CoV-2 3CLpro and anti-COVID-19 drug discovery from medicinal plants. J. Pharm. Anal., 2020, 10(4), 313-319.
[http://dx.doi.org/10.1016/j.jpha.2020.03.009] [PMID: 32296570]
[27]
Xu, Z.; Peng, C.; Shi, Y.; Zhu, Z.; Mu, K.; Wang, X. Nelfinavir was predicted to be a potential inhibitor of 2019-nCov main protease by an integrative approach combining homology modelling, molecular docking and binding free energy calculation. bioRxiv, 2020.
[http://dx.doi.org/10.1101/2020.01.27.921627]
[28]
Sheahan, T.P.; Sims, A.C.; Leist, S.R.; Schäfer, A.; Won, J.; Brown, A.J.; Montgomery, S.A.; Hogg, A.; Babusis, D.; Clarke, M.O.; Spahn, J.E.; Bauer, L.; Sellers, S.; Porter, D.; Feng, J.Y.; Cihlar, T.; Jordan, R.; Denison, M.R.; Baric, R.S. Comparative therapeutic efficacy of remdesivir and combination lopinavir, ritonavir, and interferon beta against MERS-CoV. Nat. Commun., 2020, 11(1), 222.
[http://dx.doi.org/10.1038/s41467-019-13940-6] [PMID: 31924756]
[29]
Zhang, L.; Lin, D.; Sun, X.; Curth, U.; Drosten, C. Sauerhering, L Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved a-ketoamide inhibitors. Science, 2020, 368(6489), 409-412.
[30]
Jin, Z.; Du, X.; Xu, Y.; Deng, Y.; Liu, M.; Zhao, Y.; Zhang, B.; Li, X.; Zhang, L.; Peng, C.; Duan, Y.; Yu, J.; Wang, L.; Yang, K.; Liu, F.; Jiang, R.; Yang, X.; You, T.; Liu, X.; Yang, X.; Bai, F.; Liu, H.; Liu, X.; Guddat, L.W.; Xu, W.; Xiao, G.; Qin, C.; Shi, Z.; Jiang, H.; Rao, Z.; Yang, H. Structure of M pro from COVID-19 virus and discovery of its inhibitors. Nature, 2020, 582(7811), 289-293.
[http://dx.doi.org/10.1038/s41586-020-2223-y]
[31]
Chang, M.W.; Ayeni, C.; Breuer, S.; Torbett, B.E. Virtual screening for HIV protease inhibitors: A comparison of AutoDock 4 and Vina. PLoS One, 2010, 5(8), e11955.
[http://dx.doi.org/10.1371/journal.pone.0011955] [PMID: 20694138]
[32]
Kumari, R.; Kumar, R.; Lynn, A. Open Source Drug Discovery Consortium. g_mmpbsa-a GROMACS tool for high-throughput MM-PBSA calculations. J. Chem. Inf. Model., 2014, 54(7), 1951-1962.
[http://dx.doi.org/10.1021/ci500020m] [PMID: 24850022]
[33]
He, M.M.; Smith, A.S.; Oslob, J.D.; Flanagan, W.M.; Braisted, A.C.; Whitty, A.; Cancilla, M.T.; Wang, J.; Lugovskoy, A.A.; Yoburn, J.C.; Fung, A.D.; Farrington, G.; Eldredge, J.K.; Day, E.S.; Cruz, L.A.; Cachero, T.G.; Miller, S.K.; Friedman, J.E.; Choong, I.C.; Cunningham, B.C. Small-molecule inhibition of TNF-alpha. Science, 2005, 310(5750), 1022-1025.
[http://dx.doi.org/10.1126/science.1116304] [PMID: 16284179]
[34]
Vigers, G.P.A.; Anderson, L.J.; Caffes, P.; Brandhuber, B.J. Crystal structure of the type-I interleukin-1 receptor complexed with interleukin-1β. Nature, 1997, 386(6621), 190-194.
[http://dx.doi.org/10.1038/386190a0] [PMID: 9062193]
[35]
Somers, W.; Stahl, M.; Seehra, J.S. 1.9 A crystal structure of interleukin 6: Implications for a novel mode of receptor dimerization and signaling. EMBO J., 1997, 16(5), 989-997.
[http://dx.doi.org/10.1093/emboj/16.5.989] [PMID: 9118960]
[36]
Protein Data Bank. RCSB PDB: Homepage. Rcsb Pdb. 2019.
[37]
Iaust, S.; Horby, P.; Lim, W.S.; Emberson, J.; Mafham, M.; Bell, J.; Linsell, L. Effect of dexamethasone in hospitalized patients with COVID-19: Preliminary report. Med. Rxiv, 2020.
[38]
Zoete, V.; Daina, A.; Bovigny, C.; Michielin, O. SwissSimilarity: A web tool for low to ultra high throughput ligand-based virtual screening. J. Chem. Inf. Model., 2016, 56(8), 1399-1404.
[http://dx.doi.org/10.1021/acs.jcim.6b00174] [PMID: 27391578]
[39]
O’Boyle, N.M.; Banck, M.; James, C.A.; Morley, C.; Vandermeersch, T.; Hutchison, G.R. Open Babel: An open chemical toolbox. J. Cheminform., 2011, 3(1), 33.
[http://dx.doi.org/10.1186/1758-2946-3-33] [PMID: 21982300]
[40]
Daina, A.; Michielin, O.; Zoete, V. SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci. Rep., 2017, 7(1), 42717.
[http://dx.doi.org/10.1038/srep42717] [PMID: 28256516]
[41]
Stower, H. Lopinavir-ritonavir in severe COVID-19. Nat. Med., 2020, 26(4), 465.
[PMID: 32273604]
[42]
Kim, J.; Jung, J.; Kim, T.H.; Kang, N.; Choi, H.; Oh, D.H.; Ahn, M.Y.; Kim, S.H.; Hahm, C.; Lee, Y.K.; Park, K.; Hong, K.; Choi, J.P. Pneumonia-targeted lopinavir/ritonavir-based treatment for patients with COVID-19: An early-period retrospective single center observational study. BMC Infect. Dis., 2021, 21(1), 952.
[http://dx.doi.org/10.1186/s12879-021-06588-5] [PMID: 34521365]
[43]
Xue, X.; Yu, H.; Yang, H.; Xue, F.; Wu, Z.; Shen, W.; Li, J.; Zhou, Z.; Ding, Y.; Zhao, Q.; Zhang, X.C.; Liao, M.; Bartlam, M.; Rao, Z. Structures of two coronavirus main proteases: Implications for substrate binding and antiviral drug design. J. Virol., 2008, 82(5), 2515-2527.
[http://dx.doi.org/10.1128/JVI.02114-07] [PMID: 18094151]
[44]
Ren, Z.; Yan, L.; Zhang, N.; Guo, Y.; Yang, C.; Lou, Z.; Rao, Z. The newly emerged SARS-like coronavirus HCoV-EMC also has an “Achilles’ heel”: Current effective inhibitor targeting a 3C-like protease. Protein Cell, 2013, 4(4), 248-250.
[http://dx.doi.org/10.1007/s13238-013-2841-3] [PMID: 23549610]
[45]
Banerjee, P.; Eckert, A.O.; Schrey, A.K.; Preissner, R. ProTox-II: A webserver for the prediction of toxicity of chemicals. Nucleic Acids Res., 2018, 46(W1), W257-W263.
[http://dx.doi.org/10.1093/nar/gky318] [PMID: 29718510]
[46]
Abraham, M.J.; Murtola, T.; Schulz, R.; Páll, S.; Smith, J.C.; Hess, B. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 2015, 1-2, 19-25.
[47]
Sousa da Silva, A.W.; Vranken, W.F. ACPYPE - AnteChamber python parser interfacE. BMC Res. Notes, 2012, 5(1), 367.
[http://dx.doi.org/10.1186/1756-0500-5-367] [PMID: 22824207]
[48]
Bussi, G.; Donadio, D.; Parrinello, M. Canonical sampling through velocity rescaling. J. Chem. Phys., 2007, 126(1), 014101.
[http://dx.doi.org/10.1063/1.2408420] [PMID: 17212484]
[49]
Parrinello, M.; Rahman, A. Polymorphic transitions in single crystals: A new molecular dynamics method. J. Appl. Phys., 1981, 52(12), 7182-7190.
[http://dx.doi.org/10.1063/1.328693]
[50]
Hess, B.; Bekker, H.; Berendsen, H.J.C.; Fraaije, J.G.E.M. LINCS: A linear constraint solver for molecular simulations. J. Comput. Chem., 1997, 18(12), 1463-1472.
[http://dx.doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463:AID-JCC4>3.0.CO;2-H]
[51]
Wang, E.; Sun, H.; Wang, J.; Wang, Z.; Liu, H.; Zhang, J.Z.H.; Hou, T. End-point binding free energy calculation with MM/PBSA and MM/GBSA: Strategies and applications in drug design. Chem. Rev., 2019, 119(16), 9478-9508.
[http://dx.doi.org/10.1021/acs.chemrev.9b00055] [PMID: 31244000]
[52]
Laskowski, R.A.; Swindells, M.B. LigPlot+: Multiple ligand-protein interaction diagrams for drug discovery. J. Chem. Inf. Model., 2011, 51(10), 2778-2786.
[http://dx.doi.org/10.1021/ci200227u] [PMID: 21919503]
[53]
Qais, F.A.; Sarwar, T.; Ahmad, I.; Khan, R.A.; Shahzad, S.A.; Husain, F.M. Glyburide inhibits non-enzymatic glycation of HSA: An approach for the management of AGEs associated diabetic complications. Int. J. Biol. Macromol., 2021, 169, 143-152.
[http://dx.doi.org/10.1016/j.ijbiomac.2020.12.096] [PMID: 33338529]
[54]
Rath, B.; Abul Qais, F.; Patro, R.; Mohapatra, S.; Sharma, T. Design, synthesis and molecular modeling studies of novel mesalamine linked coumarin for treatment of inflammatory bowel disease. Bioorg. Med. Chem. Lett., 2021, 41(Apr), 128029.
[http://dx.doi.org/10.1016/j.bmcl.2021.128029] [PMID: 33839254]
[55]
Fouedjou, R.T.; Chtita, S.; Bakhouch, M.; Belaidi, S.; Ouassaf, M.; Djoumbissie, L.A.; Tapondjou, L.A.; Abul Qais, F. Cameroonian medicinal plants as potential candidates of SARS-CoV-2 inhibitors. J. Biomol. Struct. Dyn., 2021, (Apr), 1-15.
[http://dx.doi.org/10.1080/07391102.2021.1914170] [PMID: 33908318]
[56]
Miller, B.R., III; McGee, T.D., Jr; Swails, J.M.; Homeyer, N.; Gohlke, H.; Roitberg, A.E. MMPBSA.py: An efficient program for end-state free energy calculations. J. Chem. Theory Comput., 2012, 8(9), 3314-3321.
[http://dx.doi.org/10.1021/ct300418h] [PMID: 26605738]

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