Abstract
Introduction: The novel coronavirus disease (COVID-19) is a viral disease caused by severe acute respiratory syndrome coronavirus 2 (SAR-CoV-2). The development of antiviral drugs has enhaced treatment of COVID-19. SARS-CoV-2 main protease (Mpro) is a key enzyme responsible for viral replication and transcription. This study aimed to identify new natural structures for the design of SARS-CoV-2 Mpro inhibitors.
Methods: In this present work, The CDOCKER protocol and scoring functions were validated. The validated docking-based virtual screening approach was then employed to search the in-house database of natural compounds for potential lead compounds as SARS-CoV-2 Mpro inhibitors. The top 3 compounds were further biologically evaluated in vitro.
Results and Discussion: Docking studies of the known ligand GC-376 led to results consistent with cocrystallized data (PDB ID: 7D1M). Additionally, the effectiveness of docking scoring functions was validated by using the training set consisting of 15 active compounds and 15 inactive compounds. Then, the in-house database of natural compounds (overall 34,439 natural compounds) was subjected to dockingbased virtual screening resulting in the identification of the top 100 compounds having relatively better docking scores. Among them, the highest ranking 3 compounds (W-1, W-2, and W-3) were biologically evaluated in vitro for their inhibitory activity against SARS-CoV-2 Mpro, and compound W-1 was identified as the most potent SARS-CoV-2 Mpro inhibitor with an IC50 value of 63 ± 3 μM. Interestingly, it appeared that the in vitro activities of compounds W-1, W-2, and W-3 were in agreement with their molecular modeling data.
Conclusion: Our results provided a useful reference for the discovery of novel natural SARS-CoV-2 Mpro inhibitors by virtual screening.
[1]
Kumar, A.; Prasoon, P.; Kumari, C.; Pareek, V.; Faiq, M.A.; Narayan, R.K.; Kulandhasamy, M.; Kant, K. SARS‐CoV‐2‐specific virulence factors in COVID‐19. J. Med. Virol., 2021, 93(3), 1343-1350.
[http://dx.doi.org/10.1002/jmv.26615] [PMID: 33085084]
[http://dx.doi.org/10.1002/jmv.26615] [PMID: 33085084]
[2]
Chams, N.; Chams, S.; Badran, R.; Shams, A.; Araji, A.; Raad, M.; Mukhopadhyay, S.; Stroberg, E.; Duval, E.J.; Barton, L.M.; Hajj Hussein, I. COVID-19: A multidisciplinary review. Front. Public Health, 2020, 8, 383.
[http://dx.doi.org/10.3389/fpubh.2020.00383] [PMID: 32850602]
[http://dx.doi.org/10.3389/fpubh.2020.00383] [PMID: 32850602]
[3]
Arya, R.; Kumari, S.; Pandey, B.; Mistry, H.; Bihani, S.C.; Das, A.; Prashar, V.; Gupta, G.D.; Panicker, L.; Kumar, M. Structural insights into SARS-CoV-2 proteins. J. Mol. Biol., 2021, 433(2), 166725.
[http://dx.doi.org/10.1016/j.jmb.2020.11.024] [PMID: 33245961]
[http://dx.doi.org/10.1016/j.jmb.2020.11.024] [PMID: 33245961]
[4]
Agbowuro, A.A.; Huston, W.M.; Gamble, A.B.; Tyndall, J.D.A. Proteases and protease inhibitors in infectious diseases. Med. Res. Rev., 2018, 38(4), 1295-1331.
[http://dx.doi.org/10.1002/med.21475] [PMID: 29149530]
[http://dx.doi.org/10.1002/med.21475] [PMID: 29149530]
[5]
Dong, S.; Sun, J.; Mao, Z.; Wang, L.; Lu, Y.L.; Li, J. A guideline for homology modeling of the proteins from newly discovered betacoronavirus, 2019 novel coronavirus (2019‐nCoV). J. Med. Virol., 2020, 92(9), 1542-1548.
[http://dx.doi.org/10.1002/jmv.25768] [PMID: 32181901]
[http://dx.doi.org/10.1002/jmv.25768] [PMID: 32181901]
[6]
Sabbah, D.A.; Hajjo, R.; Bardaweel, S.K.; Zhong, H.A. An updated review on SARS-CoV-2 main proteinase (MPro): Protein structure and small-molecule inhibitors. Curr. Top. Med. Chem., 2021, 21(6), 442-460.
[http://dx.doi.org/10.2174/18734294MTEy0MDk6w] [PMID: 33292134]
[http://dx.doi.org/10.2174/18734294MTEy0MDk6w] [PMID: 33292134]
[7]
Zhao, Y.; Fang, C.; Zhang, Q.; Zhang, R.; Zhao, X.; Duan, Y.; Wang, H.; Zhu, Y.; Feng, L.; Zhao, J.; Shao, M.; Yang, X.; Zhang, L.; Peng, C.; Yang, K.; Ma, D.; Rao, Z.; Yang, H. Crystal structure of SARS-CoV-2 main protease in complex with protease inhibitor PF-07321332. Protein Cell, 2022, 13(9), 689-693.
[http://dx.doi.org/10.1007/s13238-021-00883-2] [PMID: 34687004]
[http://dx.doi.org/10.1007/s13238-021-00883-2] [PMID: 34687004]
[8]
Lockbaum, G.J.; Reyes, A.C.; Lee, J.M.; Tilvawala, R.; Nalivaika, E.A.; Ali, A.; Kurt Yilmaz, N.; Thompson, P.R.; Schiffer, C.A. Crystal structure of SARS-CoV-2 main protease in complex with the non-covalent inhibitor ML188. Viruses, 2021, 13(2), 174.
[http://dx.doi.org/10.3390/v13020174] [PMID: 33503819]
[http://dx.doi.org/10.3390/v13020174] [PMID: 33503819]
[9]
Li, J.; Zhou, X.; Zhang, Y.; Zhong, F.; Lin, C.; McCormick, P.J.; Jiang, F.; Luo, J.; Zhou, H.; Wang, Q.; Fu, Y.; Duan, J.; Zhang, J. Crystal structure of SARS-CoV-2 main protease in complex with the natural product inhibitor shikonin illuminates a unique binding mode. Sci. Bull., 2021, 66(7), 661-663.
[http://dx.doi.org/10.1016/j.scib.2020.10.018] [PMID: 33163253]
[http://dx.doi.org/10.1016/j.scib.2020.10.018] [PMID: 33163253]
[10]
Amin, S.A.; Banerjee, S.; Ghosh, K.; Gayen, S.; Jha, T. Protease targeted COVID-19 drug discovery and its challenges: Insight into viral main protease (Mpro) and papain-like protease (PLpro) inhibitors. Bioorg. Med. Chem., 2021, 29, 115860.
[http://dx.doi.org/10.1016/j.bmc.2020.115860] [PMID: 33191083]
[http://dx.doi.org/10.1016/j.bmc.2020.115860] [PMID: 33191083]
[11]
Hayek-Orduz, Y.; Vásquez, A.F.; Villegas-Torres, M.F.; Caicedo, P.A.; Achenie, L.E.K.; González Barrios, A.F. Novel covalent and non-covalent complex-based pharmacophore models of SARS-CoV-2 main protease (Mpro) elucidated by microsecond MD simulations. Sci. Rep., 2022, 12(1), 14030.
[http://dx.doi.org/10.1038/s41598-022-17204-0] [PMID: 35982147]
[http://dx.doi.org/10.1038/s41598-022-17204-0] [PMID: 35982147]
[12]
Xu, L.; Xie, L.; Zhang, D.; Xu, X. Elucidation of binding features and dissociation pathways of inhibitors and modulators in SARS-CoV-2 main protease by multiple molecular dynamics simulations. Molecules, 2022, 27(20), 6823.
[http://dx.doi.org/10.3390/molecules27206823] [PMID: 36296416]
[http://dx.doi.org/10.3390/molecules27206823] [PMID: 36296416]
[13]
Saikia, S.; Bordoloi, M. Molecular docking: Challenges, advances and its use in drug discovery perspective. Curr. Drug Targets, 2019, 20(5), 501-521.
[http://dx.doi.org/10.2174/1389450119666181022153016] [PMID: 30360733]
[http://dx.doi.org/10.2174/1389450119666181022153016] [PMID: 30360733]
[14]
Elzupir, A.O. Inhibition of SARS-CoV-2 main protease 3CLpro by means of α-ketoamide and pyridone-containing pharmaceuticals using in silico molecular docking. J. Mol. Struct., 2020, 1222, 128878.
[http://dx.doi.org/10.1016/j.molstruc.2020.128878] [PMID: 32834113]
[http://dx.doi.org/10.1016/j.molstruc.2020.128878] [PMID: 32834113]
[15]
Cetin, A. In silico studies on stilbenolignan analogues as SARS-CoV-2 Mpro inhibitors. Chem. Phys. Lett., 2021, 771, 138563.
[http://dx.doi.org/10.1016/j.cplett.2021.138563] [PMID: 33776065]
[http://dx.doi.org/10.1016/j.cplett.2021.138563] [PMID: 33776065]
[16]
da Silva, J.K.R.; Figueiredo, P.L.B.; Byler, K.G.; Setzer, W.N. Essential oils as antiviral agents. Potential of essential oils to treat SARS-CoV-2 infection: An in-silico investigation. Int. J. Mol. Sci., 2020, 21(10), 3426.
[http://dx.doi.org/10.3390/ijms21103426] [PMID: 32408699]
[http://dx.doi.org/10.3390/ijms21103426] [PMID: 32408699]
[17]
Khater, I.; Nassar, A. In silico molecular docking analysis for repurposing approved antiviral drugs against SARS-CoV-2 main protease. Biochem. Biophys. Rep., 2021, 27, 101032.
[http://dx.doi.org/10.1016/j.bbrep.2021.101032] [PMID: 34099985]
[http://dx.doi.org/10.1016/j.bbrep.2021.101032] [PMID: 34099985]
[18]
Amendola, G.; Ettari, R.; Previti, S.; Di Chio, C.; Messere, A.; Di Maro, S.; Hammerschmidt, S.J.; Zimmer, C.; Zimmermann, R.A.; Schirmeister, T.; Zappalà, M.; Cosconati, S. Lead discovery of SARS-CoV-2 main protease inhibitors through covalent docking-based virtual screening. J. Chem. Inf. Model., 2021, 61(4), 2062-2073.
[http://dx.doi.org/10.1021/acs.jcim.1c00184] [PMID: 33784094]
[http://dx.doi.org/10.1021/acs.jcim.1c00184] [PMID: 33784094]
[19]
Fu, L.; Ye, F.; Feng, Y.; Yu, F.; Wang, Q.; Wu, Y.; Zhao, C.; Sun, H.; Huang, B.; Niu, P.; Song, H.; Shi, Y.; Li, X.; Tan, W.; Qi, J.; Gao, G.F. Both Boceprevir and GC376 efficaciously inhibit SARS-CoV-2 by targeting its main protease. Nat. Commun., 2020, 11(1), 4417.
[http://dx.doi.org/10.1038/s41467-020-18233-x] [PMID: 32887884]
[http://dx.doi.org/10.1038/s41467-020-18233-x] [PMID: 32887884]
[20]
Bertaccini, E.J.; Yoluk, O.; Lindahl, E.R.; Trudell, J.R. Assessment of homology templates and an anesthetic binding site within the γ-aminobutyric acid receptor. Anesthesiology, 2013, 119(5), 1087-1095.
[http://dx.doi.org/10.1097/ALN.0b013e31829e47e3] [PMID: 23770602]
[http://dx.doi.org/10.1097/ALN.0b013e31829e47e3] [PMID: 23770602]
[21]
Luttens, A.; Gullberg, H.; Abdurakhmanov, E.; Vo, D.D.; Akaberi, D.; Talibov, V.O.; Nekhotiaeva, N.; Vangeel, L.; De Jonghe, S.; Jochmans, D.; Krambrich, J.; Tas, A.; Lundgren, B.; Gravenfors, Y.; Craig, A.J.; Atilaw, Y.; Sandström, A.; Moodie, L.W.K.; Lundkvist, Å.; van Hemert, M.J.; Neyts, J.; Lennerstrand, J.; Kihlberg, J.; Sandberg, K.; Danielson, U.H.; Carlsson, J. Ultralarge virtual screening identifies SARS-CoV-2 main protease inhibitors with broad-spectrum activity against coronaviruses. J. Am. Chem. Soc., 2022, 144(7), 2905-2920.
[http://dx.doi.org/10.1021/jacs.1c08402] [PMID: 35142215]
[http://dx.doi.org/10.1021/jacs.1c08402] [PMID: 35142215]
[22]
Clyde, A.; Galanie, S.; Kneller, D.W.; Ma, H.; Babuji, Y.; Blaiszik, B.; Brace, A.; Brettin, T.; Chard, K.; Chard, R.; Coates, L.; Foster, I.; Hauner, D.; Kertesz, V.; Kumar, N.; Lee, H.; Li, Z.; Merzky, A.; Schmidt, J.G.; Tan, L.; Titov, M.; Trifan, A.; Turilli, M.; Van Dam, H.; Chennubhotla, S.C.; Jha, S.; Kovalevsky, A.; Ramanathan, A.; Head, M.S.; Stevens, R. High-throughput virtual screening and validation of a SARS-CoV-2 main protease noncovalent inhibitor. J. Chem. Inf. Model., 2022, 62(1), 116-128.
[http://dx.doi.org/10.1021/acs.jcim.1c00851] [PMID: 34793155]
[http://dx.doi.org/10.1021/acs.jcim.1c00851] [PMID: 34793155]
[23]
Jiménez-Avalos, G.; Vargas-Ruiz, A.P.; Delgado-Pease, N.E.; Olivos-Ramirez, G.E.; Sheen, P.; Fernández-Díaz, M.; Quiliano, M.; Zimic, M.; Agurto-Arteaga, A.; Antiparra, R.; Ardiles-Reyes, M.; Calderon, K.; Cauna-Orocollo, Y.; de Grecia Cauti-Mendoza, M.; Chipana-Flores, N.; Choque-Guevara, R.; Chunga-Girón, X.; Criollo-Orozco, M.; De La Cruz, L.; Delgado-Ccancce, E.; Elugo-Guevara, C.; Fernández-Sanchez, M.; Guevara-Sarmiento, L.; Gutiérrez, K.; Heredia-Almeyda, O.; Huaccachi-Gonzalez, E.; Huerta-Roque, P.; Icochea, E.; Isasi-Rivas, G.; Juscamaita-Bartra, R.A.; Licla-Inca, A.; Montalvan, A.; Montesinos-Millan, R.; Núñez-Fernández, D.; Ochoa-Ortiz, A.; Páucar-Montoro, E.; Pauyac, K.; Perez-Martinez, J.L.; Perez-M, N.; Poma-Acevedo, A.; Quiñones-Garcia, S.; Ramirez-Ortiz, I.; Ramos-Sono, D.; Rios-Angulo, A.A.; Rios-Matos, D.; Rojas-Neyra, A.; Romero, Y.K.; Salguedo-Bohorquez, M.I.; Sernaque-Aguilar, Y.; Soto, L.F.; Tataje-Lavanda, L.; Ticona, J.; Vallejos-Sánchez, K.; Villanueva-Pérez, D.; Ygnacio-Aguirre, F. Comprehensive virtual screening of 4.8 k flavonoids reveals novel insights into allosteric inhibition of SARS-CoV-2 MPRO. Sci. Rep., 2021, 11(1), 15452.
[http://dx.doi.org/10.1038/s41598-021-94951-6] [PMID: 34326429]
[http://dx.doi.org/10.1038/s41598-021-94951-6] [PMID: 34326429]
[24]
Rossetti, G.G.; Ossorio, M.A.; Rempel, S.; Kratzel, A.; Dionellis, V.S.; Barriot, S. Tropia, L.; Gorgulla, C.; Arthanari, H.; Thiel, V.; Mohr, P.; Gamboni, R.; Halazonetis, T.D. Non-covalent SARS-CoV-2 Mpro inhibitors developed from in silico screen hits. Sci. Rep., 2022, 12(1), 2505.
[http://dx.doi.org/10.1038/s41598-022-06306-4] [PMID: 35169179]
[http://dx.doi.org/10.1038/s41598-022-06306-4] [PMID: 35169179]
[25]
Ding, X.; Hayes, R.L.; Vilseck, J.Z.; Charles, M.K.; Brooks, C.L. III CDOCKER and $${λ$$-dynamics for prospective prediction in D3R Grand Challenge 2. J. Comput. Aided Mol. Des., 2018, 32(1), 89-102.
[http://dx.doi.org/10.1007/s10822-017-0050-5] [PMID: 28884249]
[http://dx.doi.org/10.1007/s10822-017-0050-5] [PMID: 28884249]
[26]
Kumar, S.B.; Krishna, S.; Pradeep, S.; Mathews, D.E.; Pattabiraman, R.; Murahari, M.; Murthy, T.P.K. Screening of natural compounds from Cyperus rotundus Linn against SARS-CoV-2 main protease (Mpro): An integrated computational approach. Comput. Biol. Med., 2021, 134, 104524.
[http://dx.doi.org/10.1016/j.compbiomed.2021.104524] [PMID: 34090015]
[http://dx.doi.org/10.1016/j.compbiomed.2021.104524] [PMID: 34090015]
[27]
Wang, S.; Jiang, J.H.; Li, R.Y.; Deng, P. Docking-based virtual screening of TβR1 inhibitors: Evaluation of pose prediction and scoring functions. BMC Chem., 2020, 14(1), 52.
[http://dx.doi.org/10.1186/s13065-020-00704-3] [PMID: 32818203]
[http://dx.doi.org/10.1186/s13065-020-00704-3] [PMID: 32818203]
[28]
Qiao, J.; Li, Y.S.; Zeng, R.; Liu, F.L.; Luo, R.H.; Huang, C.; Wang, Y.F.; Zhang, J.; Quan, B.; Shen, C.; Mao, X.; Liu, X.; Sun, W.; Yang, W.; Ni, X.; Wang, K.; Xu, L.; Duan, Z.L.; Zou, Q.C.; Zhang, H.L.; Qu, W.; Long, Y.H.P.; Li, M.H.; Yang, R.C.; Liu, X.; You, J.; Zhou, Y.; Yao, R.; Li, W.P.; Liu, J.M.; Chen, P.; Liu, Y.; Lin, G.F.; Yang, X.; Zou, J.; Li, L.; Hu, Y.; Lu, G.W.; Li, W.M.; Wei, Y.Q.; Zheng, Y.T.; Lei, J.; Yang, S. SARS-CoV-2 M pro inhibitors with antiviral activity in a transgenic mouse model. Science, 2021, 371(6536), 1374-1378.
[http://dx.doi.org/10.1126/science.abf1611] [PMID: 33602867]
[http://dx.doi.org/10.1126/science.abf1611] [PMID: 33602867]
[29]
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 Mpro from SARS-CoV-2 and discovery of its inhibitors. Nature, 2020, 582(7811), 289-293.
[http://dx.doi.org/10.1038/s41586-020-2223-y] [PMID: 32272481]
[http://dx.doi.org/10.1038/s41586-020-2223-y] [PMID: 32272481]
[30]
Kumar, B.K.; Sekhar, K.V.G.C.; Kunjiappan, S.; Jamalis, J.; Balaña-Fouce, R.; Tekwani, B.L.; Sankaranarayanan, M. Druggable targets of SARS-CoV-2 and treatment opportunities for COVID-19. Bioorg. Chem., 2020, 104, 104269.
[31]
Zhang, L.; Lin, D.; Sun, X.; Curth, U.; Drosten, C.; Sauerhering, L.; Becker, S. Rox, K.; Hilgenfeld, R. Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors. Science, 2020, 368(6489), 409-412.
[http://dx.doi.org/10.1126/science.abb3405] [PMID: 32198291]
[http://dx.doi.org/10.1126/science.abb3405] [PMID: 32198291]
[32]
Li, Q.; Kang, C. Progress in developing inhibitors of SARS-CoV-2 3C-like protease. Microorganisms, 2020, 8(8), 1250.
[http://dx.doi.org/10.3390/microorganisms8081250] [PMID: 32824639]
[http://dx.doi.org/10.3390/microorganisms8081250] [PMID: 32824639]
[33]
Gimeno, A.; Mestres-Truyol, J.; Ojeda-Montes, M.J.; Macip, G.; Saldivar-Espinoza, B.; Cereto-Massagué, A.; Pujadas, G.; Garcia-Vallvé, S. Prediction of novel inhibitors of the main protease (M-pro) of SARS-CoV-2 through consensus docking and drug reposition. Int. J. Mol. Sci., 2020, 21(11), 3793.
[http://dx.doi.org/10.3390/ijms21113793] [PMID: 32471205]
[http://dx.doi.org/10.3390/ijms21113793] [PMID: 32471205]
[34]
Vatansever, E.C.; Yang, K.S.; Drelich, A.K.; Kratch, K.C.; Cho, C.C.; Kempaiah, K.R.; Hsu, J.C.; Mellott, D.M.; Xu, S.; Tseng, C.T.K.; Liu, W.R. Bepridil is potent against SARS-CoV-2 in vitro. Proc. Natl. Acad. Sci. USA, 2021, 118(10), e2012201118.
[http://dx.doi.org/10.1073/pnas.2012201118] [PMID: 33597253]
[http://dx.doi.org/10.1073/pnas.2012201118] [PMID: 33597253]
[35]
Sureja, D.K.; Shah, A.P.; Gajjar, N.D.; Jadeja, S.B.; Bodiwala, K.B.; Dhameliya, T.M. In-silico computational investigations of antiViral lignan derivatives as potent inhibitors of SARS CoV-2. ChemistrySelect, 2022, 7(28), e202202069.
[http://dx.doi.org/10.1002/slct.202202069] [PMID: 35942360]
[http://dx.doi.org/10.1002/slct.202202069] [PMID: 35942360]
[36]
Liu, X.; Zhao, J.; Qiu, G.; Alahmadi, T.A.; Alharbi, S.A.; Wainwright, M.; Duan, W. Biological activities of some natural compounds and their cytotoxicity studies against breast and prostate cancer cell lines and anti-COVID19 studies. J. Oleo Sci., 2022, 71(4), 587-597.
[http://dx.doi.org/10.5650/jos.ess21275] [PMID: 35370217]
[http://dx.doi.org/10.5650/jos.ess21275] [PMID: 35370217]
[37]
Gogoi, N.; Chowdhury, P.; Goswami, A.K.; Das, A.; Chetia, D.; Gogoi, B. Computational guided identification of a citrus flavonoid as potential inhibitor of SARS-CoV-2 main protease. Mol. Divers., 2021, 25(3), 1745-1759.
[http://dx.doi.org/10.1007/s11030-020-10150-x] [PMID: 33236176]
[http://dx.doi.org/10.1007/s11030-020-10150-x] [PMID: 33236176]
