In Silico Comparison of Main Proteinase Inhibitors for Different Coronaviruses
DOI:
https://doi.org/10.21123/bsj.2024.9091Keywords:
CoV-19, Cystine protease, Main proteinase, Molecular docking, Natural productsAbstract
Abstract
Coronaviruses are enclosed positive stranded RNA viruses with spike protein protrusions that permit the virus to penetrate and affect host cells. The emergence of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Middle East Respiratory Syndrome Coronavirus (MERS-CoV), as mortal human CoV illnesses, has sparked considerable interest in the medical community. The fast and global outbreak of a novel human coronavirus generated by a novel progeny of coronavirus 2 (CoV-2) has promoted an urgent need to identify an effective target for COVID-19 treatment. The main proteinase MPro has been prominented as an appealing therapeutic target for coronaviruses, which is responsible for the transcriptase and replicase of coronaviruses. The identification of prospective medications is an imperative and critical need for the medical community. Molecular docking was used to describe the protease and asses the capacity of various well-known and laboratory-tested natural MPro inhibitors. Seventy-sixth natural compounds with known inhibitory activity and four medicines reported against CoV-1 were chosen for molecular docking study. Our in-silico studies reveal that many of these molecules show high binding affinity for several CoV-2 proteases and compare favorably to CoV-1 and MERS proteases. Our research indicates that these molecules could be anti CoV-2 MPro. implying their possibility for reprofiling as antiviral leads with broad scope.
Received 19/05/2023
Revised 21/07/2023
Accepted 23/07/2023
Published Online First 20/01/2024
References
Shereen MA, Khan S, Kazmi A, Bashir N, Siddique R. COVID-19 infection: Emergence, transmission, and characteristics of human coronaviruses. J Adv Res. 2020; 24: 91-98.https://doi.org/10.1016/j.jare.2020.03.005
Rothan HA, Byrareddy SN. The epidemiology and pathogenesis of coronavirus disease (COVID-19) outbreak. J Autoimmun. 2020; 109: 102433. https://doi.org/10.1016/j.jaut.2020.102433
Ye ZW, Yuan S, Yuen KS, Fung SY, Chan CP, Jin DY. Zoonotic origins of human coronaviruses. Int J Biol Sci. 2020; 16 (1): 1686-1697. https://doi.org/10.7150/ijbs.45472
Sabbah DA, Hajjo R, Bardaweel SK, Zhong HA. An updated review on betacoronavirus viral entry inhibitors: learning from past discoveries to advance COVID-19 drug discovery. Curr Top Med Chem. 2021; 21 (7): 571-596. https://doi.org/10.2174/1568026621666210119111409
Shirato K, Melaku SK, Kawachi K, Nao N, Iwata-Yoshikawa N, Kawase M, et al. Middle East respiratory syndrome coronavirus in dromedaries in Ethiopia is antigenically different from the Middle East isolate EMC Front Microbiol. 2019; 10: 1326.https://doi.org/10.3389/fmicb.2019.01326
Mann R, Perisetti A, Gajendran M, Gandhi Z, Umapathy C, Goyal H. Clinical characteristics, diagnosis, and treatment of major coronavirus outbreaks. Front Med. 2020; 7: 581521. https://doi.org/10.3389/fmed.2020.581521
Organization WH. Naming the coronavirus disease (COVID-19) and the virus that causes it. Braz J Implantol Health Sci. 2020; 2(3): 2020. https://bjihs.emnuvens.com.br/bjihs/article/view/173
Devi S, Raj A, Kumar P. Corona Virus: A detail Study on Covid-19. Covid 19: Impact and Response Volume II. 1st ed. Maharashtra India: Bhumi Publishing; 2021. 53p.
Chan JF-W, Kok K-H, Zhu Z, Chu H, To KK-W, Yuan S, et al. Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. Emerg. microbes infect. 2020; 9 (1): 221-236.https://doi.org/10.1080/22221751.2020.1719902
Prajapat M, Sarma P, Shekhar N, Avti P, Sinha S, Kaur H, et al. Drug targets for corona virus: A systematic review. Indian J Pharmacol. 2020; 52(1): 56-65. https://doi.org/10.4103/ijp.IJP_115_20
Tsai PH, Wang ML, Yang DM, Liang KH, Chou SJ, Chiou SH, et al. Genomic variance of Open Reading Frames (ORFs) and Spike protein in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). J Chin Med Assoc 2020; 83 (8): 725-732.https://doi.org/10.1097/JCMA.0000000000000387
Uzunian A. Coronavirus SARS-CoV-2 and Covid-19. J Bras Patol Med Lab. 2020; 56: 1-14. https://doi.org/10.5935/1676-2444.20200053
Ng CS, Stobart CC, Luo H. Innate immune evasion mediated by picornaviral 3C protease: Possible lessons for coronaviral 3C‐like protease?. Rev Med Virol. 2021; 31 (5): 1-22. https://doi.org/10.1002/rmv.2206
Jeske L, Placzek S, Schomburg I, Chang A, Schomburg D. BRENDA in 2019: a European ELIXIR core data resource. Nucleic Acids Res. 2019; 47 (D1): D542-D549.https://doi.org/10.1093/nar/gky1048
Zhang L, Lin D, Sun X, Curth U, Drosten C, Sauerhering L, et al. Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors. Sci. 2020; 368 (6489): 409-412. https://doi.org/10.1126/science.abb3405
Ullrich S, Nitsche C. SARS‐CoV‐2 Papain‐Like Protease: Structure, Function and Inhibition. Chem Bio Chem 2022; 23 (19): e202200327.https://doi.org/10.1002/cbic.202200327
Qiu Y, Xu K. Functional studies of the coronavirus nonstructural proteins. STE Medicine 2020; 1 (2): e39-e39. https://doi.org/10.37175/stemedicine.v1i2.39
Wang KY, Liu F, Jiang R, Yang X, You T, Liu X, et al. Structure of Mpro from COVID-19 virus and discovery of its inhibitors. Nature. 2020; 582 (7811): 289-93. https://doi.org/10.1101/2020.02.26.964882
Wang M, Cao R, Zhang L, Yang X, Liu J, Xu M, et al. Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Res. 2020; 30 (3): 269-271. https://doi.org/10.1038/ s41422-020-0282-0
Lai C-C, Shih T-P, Ko W-C, Tang H-J, Hsueh P-R. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): The epidemic and the challenges. Int J Antimicrob Agents. 2020; 55 (3): 105924. https://doi.org/10.1016/j.ijantimicag.2020.105924
Morse JS, Lalonde T, Xu S, Liu WR. Learning from the past: possible urgent prevention and treatment options for severe acute respiratory infections caused by 2019‐nCoV. Chem biochem. 2020; 21 (5): 730-738. https://doi.org/10.1002/cbic.202000047
Lu H. Drug treatment options for the 2019-new coronavirus (2019-nCoV). Bio Science Trends. 2020; 14 (1): 69-71. https://doi.org/10.5582/bst.2020.01020
Elfiky AA. Natural products may interfere with SARS-CoV-2 attachment to the host cell. J Biomol Struct Dyn. 2021; 39 (9): 3194-3203. https://doi.org/10.1080/07391102.2020.1761881
Atanasov AG, Zotchev SB, Dirsch VM, Supuran CT. Natural products in drug discovery: advances and opportunities. Nat Rev Drug Discov. 2021; 20 (3): 200-216. https://doi.org/10.1038/ s41573-020-00114-z
Al-Karmalawy AA, Khattab M. Molecular modelling of mebendazole polymorphs as a potential colchicine binding site inhibitor. New J Chem. 2020; 44 (33): 13990-13996. https://doi.org/10.1039/d0nj02844d
Ghanem A, Emara HA, Muawia S, Abd El Maksoud AI, Al-Karmalawy AA, Elshal MF. Tanshinone IIA synergistically enhances the antitumor activity of doxorubicin by interfering with the PI3K/AKT/mTOR pathway and inhibition of topoisomerase II: in vitro and molecular docking studies. New J Chem. 2020; 44 (40): 17374-17381. https://doi.org/10.1039/d0nj04088f
Hussen NH. Synthesis, characterization, molecular docking, ADMET prediction, and anti-inflammatory activity of some Schiff bases derived from salicylaldehyde as a potential cyclooxygenase inhibitor. Baghdad Sci J. 2023. https://dx.doi.org/10.21123/bsj.2023.7181
Chang CC, Hsu HJ, Wu TY, Liou JW. Computer-aided discovery, design, and investigation of COVID-19 therapeutics. Tzu Chi Med J. 2022; 34 (3): 276-286. https://doi.org/10.4103/tcmj.tcmj_318_21
29. Ibrahim AA. A Theoretical Study of the Docking of Medicines with some Proteins. Baghdad Sci J. 2023; 20 (2): 0319-0319. http://dx.doi.org/10.21123/bsj.2022.7064
Majumdar S, Nandi SK, Ghosal S, Ghosh B, Mallik W, Roy ND, et al. Deep learning-based potential ligand prediction framework for COVID-19 with drug–target interaction model. Cognit Comput. 2021; 1-13. https://doi.org/10.1007/s12559-021-09840-x
Wu C-Y, Jan J-T, Ma S-H, Kuo C-J, Juan H-F, Cheng Y-SE, et al. Small molecules targeting severe acute respiratory syndrome human coronavirus. Proc Natl Acad Sci. 2004; 101 (27): 10012-10017. https://doi.org/10.1073/pnas.0403596101
Blanchard JE, Elowe NH, Huitema C, Fortin PD, Cechetto JD, Eltis LD, et al. High-throughput screening identifies inhibitors of the SARS coronavirus main proteinase. Chem Biol. 2004; 11 (10): 1445-1453. https://doi.org/10.1016/j.chembiol.2004.08.011
Kao RY, Tsui WH, Lee TS, Tanner JA, Watt RM, Huang J-D, et al. Identification of novel small-molecule inhibitors of severe acute respiratory syndrome-associated coronavirus by chemical genetics. Chem Biol. 2004; 11 (9): 1293-1299.https://doi.org/10.1016/j.chembiol.2004.07.013
Hsu JT-A, Kuo C-J, Hsieh H-P, Wang Y-C, Huang K-K, Lin CP-C, et al. Evaluation of metal-conjugated compounds as inhibitors of 3CL protease of SARS-CoV. FEBS lett. 2004; 574 (1-3): 116-120. https://doi.org/10.1016/j.febslet.2004.08.015
Shie J-J, Fang J-M, Kuo T-H, Kuo C-J, Liang P-H, Huang H-J, et al. Inhibition of the severe acute respiratory syndrome 3CL protease by peptidomimetic α, β-unsaturated esters. Bioorg Med Chem. 2005; 13 (17): 5240-5252. https://doi.org/10.1016/j.bmc.2005.05.065
Shie J-J, Fang J-M, Kuo C-J, Kuo T-H, Liang P-H, Huang H-J, et al. Discovery of potent anilide inhibitors against the severe acute respiratory syndrome 3CL protease. J Med Chem. 2005; 48 (13): 4469-4473. https://doi.org/10.1021/jm050184y
Jain RP, Pettersson HI, Zhang J, Aull KD, Fortin PD, Huitema C, et al. Synthesis and evaluation of keto-glutamine analogues as potent inhibitors of severe acute respiratory syndrome 3CLpro. J Med Chem. 2004; 47 (25): 6113-6116. https://doi.org/10.1021/jm0494873
Chen L-R, Wang Y-C, Lin YW, Chou S-Y, Chen S-F, Liu LT, et al. Synthesis and evaluation of isatin derivatives as effective SARS coronavirus 3CL protease inhibitors. Bioorg Med Chem Lett. 2005; 15 (12): 3058-3062. https://doi.org/10.1016/j.bmcl.2005.04.027
Bacha U, Barrila J, Velazquez-Campoy A, Leavitt SA, Freire E. Identification of novel inhibitors of the SARS coronavirus main protease 3CLpro. Biochem. 2004; 43 (17): 4906-4912. https://doi.org/10.1021/bi0361766
Kim JW, Cho H, Kim E, Shim SH, Yang J-L, Oh WK. Antiviral escin derivatives from the seeds of Aesculus turbinata Blume (Japanese horse chestnut). Bioorg Med Chem Lett. 2017; 27 (13): 3019-3025. https://doi.org/10.1016/j.bmcl.2017.05.022.
Fu L, Shao S, Feng Y, Ye F, Sun X, Wang Q, et al. Mechanism of microbial metabolite leupeptin in the treatment of COVID-19 by traditional chinese medicine herbs. ASM Journals. Mbio. 2021; 12 (5): e02220-21 https://doi.org/10.1128/mBio.02220-21
Downloads
Issue
Section
License
Copyright (c) 2024 Baghdad Science Journal
This work is licensed under a Creative Commons Attribution 4.0 International License.
How to Cite
