The development of papain‐like protease from SARS‐CoV‐2, a potential drug target for antiviral screening: A review

Riswanto Napitupulu(1), Is Helianti(2*), Maimunah Maimunah(3), Fairuz Andini Fatiningtyas(4), Amarila Malik(5)

(1) Faculty of Pharmacy Universitas Indonesia, Depok 16424, West Java, Indonesia
(2) Research Center of Applied Microbiology, National Agency of Research and Innovation, Cibinong Science Center, Jalan Raya Bogor Km 46, Cibinong, West Java, Indonesia
(3) Faculty of Pharmacy Universitas Indonesia, Depok 16424, West Java, Indonesia
(4) Faculty of Pharmacy Universitas Indonesia, Depok 16424, West Java, Indonesia
(5) Faculty of Pharmacy Universitas Indonesia, Depok 16424, West Java, Indonesia
(*) Corresponding Author


The SARS‐CoV‐2 outbreak caused a global pandemic, claiming numerous lives and becoming this century’s most widespread life‐threatening disease. The virus relies on two specific enzymes to facilitate replication, 3‐chymotrypsin‐like protease (3CLPro) and papain‐like protease (PLpro). These enzymes are crucial in breaking down nonstructural polypeptides into functional proteins. PLpro with LXGG↓X recognition and cleavage sites also play a role in deubiquitylase (DUB) and delSGylase by cleaving after the double glycine residue of ubiquitin (Ub) and ISG15 as a mechanism to suppress the host’s innate immune response. Despite its important role in the viral infection cycle and the potential for drug discovery, no antivirals have been approved as PLpro inhibitors. Therefore, this review focuses on PLpro protein, its recombinant product development and purification, and its application as a protein target in drug discovery for COVID‐19 screening to develop effective COVID‐19 drugs.


Drug discovery; Papain‐like protease; SARS‐CoV‐2

Full Text:



Ahmad I, Pawara R, Surana S, Patel H. 2021. The repurposed ACE2 inhibitors: SARS-CoV-2 entry blockers of Covid-19. Top. Curr. Chem. 379(6):40. doi:10.1007/s41061-021-00353-7.

Amin SA, Banerjee S, Ghosh K, Gayen S, Jha T. 2021. Protease targeted COVID-19 drug discovery and its challenges: Insight into viral main protease (Mpro) and papain-like protease (PLpro) inhibitors. Bioorg. Med. Chem. 29(August 2020):115860. doi:10.1016/j.bmc.2020.115860.

Armstrong LA, Lange SM, Cesare VD, Matthews SP, Nirujogi RS, Cole I, Hope A, Cunningham F, Toth R, Mukherjee R, Bojkova D, Gruber F, Gray D, Wyatt PG, Cinatl J, Dikic I, Davies P, Kulathu Y. 2021. Biochemical characterization of protease activity of Nsp3 from SARS-CoV-2 and its inhibition by nanobodies. PLoS ONE 16(7):e0253364. doi:10.1371/journal.pone.0253364.

Arya R, Prashar V, Kumar M. 2021. Evaluating stability and activity of SARS-CoV-2 PLpro for highthroughput screening of inhibitors. Mol. Biotechnol. 64(1):1–8. doi:10.1007/s12033-021-00383-y.

Bafna K, White K, Harish B, Rosales R, Ramelot TA, Acton TB, Moreno E, Kehrer T, Miorin L, Royer CA, García-Sastre A, Krug RM, Montelione GT. 2021. Hepatitis C virus drugs that inhibit SARS-CoV- 2 papain-like protease synergize with remdesivir to suppress viral replication in cell culture. Cell Rep. 35(7):109133. doi:10.1016/j.celrep.2021.109133.

Bai Z, Cao Y, Liu W, Li J. 2021. The SARS-CoV- 2 nucleocapsid protein and its role in viral structure, biological functions, and a potential target for drug or vaccine mitigation. Viruses 13(6):1115. doi:10.3390/v13061115.

Baum A, Fulton BO, Wloga E, Copin R, Pascal KE, Russo V, Giordano S, Lanza K, Negron N, Ni M, Wei Y, Atwal GS, Murphy AJ, Stahl N, Yancopoulos GD, Kyratsous CA. 2020. Antibody cocktail to SARS-CoV-2 spike protein prevents rapid mutational escape seen with individual antibodies. Science 369(6506):1014–1018. doi:10.1126/science.abd0831.

Beigel JH, Tomashek KM, Dodd LE, Mehta AK, Zingman BS, Kalil AC, Hohmann E, Chu HY, Luetkemeyer A, Kline S, Lopez de Castilla D, Finberg RW, Dierberg K, Tapson V, Hsieh L, Patterson TF, Paredes R, Sweeney DA, Short WR, Touloumi G, Lye DC, Ohmagari N, Oh Md, Ruiz-Palacios GM, Benfield T, Fätkenheuer G, Kortepeter MG, Atmar RL, Creech CB, Lundgren J, Babiker AG, Pett S, Neaton JD, Burgess TH, Bonnett T, Green M, Makowski M, Osinusi A, Nayak S, Lane HC. 2020. Remdesivir for the treatment of Covid-19 — Final report. N. Engl. J. Med. 383(19):1813–1826. doi:10.1056/nejmoa2007764.

Bera K, Reeda VS, Babila PR, Dinesh DC, Hritz J, Karthick T. 2021. An in silico molecular dynamics simulation study on the inhibitors of SARSCoV-2 proteases (3CLpro and PLpro) to combat COVID-19. Mol. Simul. 47(14):1168–1184. doi:10.1080/08927022.2021.1957884.

Bhatwa A, Wang W, Hassan YI, Abraham N, Li XZ, Zhou T. 2021. Challenges associated with the formation of recombinant protein inclusion bodies in Escherichia coli and strategies to address them for industrial applications. Front. Bioeng. Biotechnol. 9:630551. doi:10.3389/fbioe.2021.630551.

Cao X. 2020. COVID-19: immunopathology and its implications for therapy. Nat. Rev. Immunol. 20(5):269–270. doi:10.1038/s41577-020-0308-3.

Choi TJ, Geletu TT. 2018. High level expression and purification of recombinant flounder growth hormone in E. coli. J. Genet. Eng. Biotechnol. 16(2):347–355. doi:10.1016/j.jgeb.2018.03.006.

Copin R, Baum A, Wloga E, Pascal KE, Giordano S, Fulton BO, Zhou A, Negron N, Lanza K, Chan N, Coppola A, Chiu J, Ni M, Wei Y, Atwal GS, Hernandez AR, Saotome K, Zhou Y, Franklin MC, Hooper AT, McCarthy S, Hamon S, Hamilton JD, Staples HM, Alfson K, Carrion R, Ali S, Norton T, SomersanKarakaya S, Sivapalasingam S, Herman GA, Weinreich DM, Lipsich L, Stahl N, Murphy AJ, Yancopoulos GD, Kyratsous CA. 2021. The monoclonal antibody combination REGEN-COV protects against SARS-CoV-2 mutational escape in preclinical and human studies. Cell 184(15):3949–3961.e11. doi:10.1016/j.cell.2021.06.002.

Corti C, Crimini E, Tarantino P, Pravettoni G, Eggermont AM, Delaloge S, Curigliano G. 2021. SARS-CoV-2 vaccines for cancer patients: A call to action. Eur. J. Cancer 148:316–327. doi:10.1016/j.ejca.2021.01.046.

Coumar MS. 2021. Molecular docking for computer-aided drug design: Fundamentals, techniques, resources and applications. London: Elsevier, 1st ed edition. doi:10.1016/B978-0-12-822312-3.01001-8.

Cully M. 2022. A tale of two antiviral targets - and the COVID-19 drugs that bind them. Nat. Rev. Drug Discov 21(1):3–5. doi:10.1038/d41573-021-00202-8.

de Groot RJ, Baker SC, Baric RS, Brown CS, Drosten C, Enjuanes L, Fouchier RAM, Galiano M, Gorbalenya AE, Memish ZA, Perlman S, Poon LLM, Snijder EJ, Stephens GM, Woo PCY, Zaki AM, Zambon M, Ziebuhr J. 2013. Middle East Respiratory Syndrome Coronavirus (MERS-CoV): Announcement of the Coronavirus study group. J. Virol. 87(14):7790– 7792. doi:10.1128/jvi.01244-13.

Debnath S, Debnath B, Debnath P. 2022. Carvacrol: A PLpro Inhibitor of SARS-CoV-2 Is a Natural Weapon for COVID-19. Chem. Proc. 12(1):11. doi:10.3390/ecsoc-26-13679.

Dlamini GS, Mïller SJ, Meraba RL, Young RA, Mashiyane J, Chiwewe T, Mapiye DS. 2020. Classification of COVID-19 and other pathogenic s equences: A dinucleotide frequency and machine learning approach. IEEE Access 8:195263–195273. doi:10.1109/ACCESS.2020.3031387.

Duan K, Liu B, Li C, Zhang H, Yu T, Qu J, Zhou M, Chen L, Meng S, Hu Y, Peng C, Yuan M, Huang J, Wang Z, Yu J, Gao X, Wang D, Yu X, Li L, Zhang J, Wu X, Li B, Xu Y, Chen W, Peng Y, Hu Y, Lin L, Liu X, Huang S, Zhou Z, Zhang L, Wang Y, Zhang Z, Deng K, Xia Z, Gong Q, Zhang W, Zheng X, Liu Y, Yang H, Zhou D, Yu D, Hou J, Shi Z, Chen S, Chen Z, Zhang X, Yang X. 2020. Effectiveness of convalescent plasma therapy in severe COVID-19 patients. Proc. Natl. Acad. Sci. U. S. A. 117(17):9490–9496. doi:10.1073/pnas.2004168117.

Erlina L, Paramita RI, Kusuma WA, Fadilah F, Tedjo A, Pratomo IP, Ramadhanti NS, Nasution AK, Surado FK, Fitriawan A, Istiadi KA, Yanuar A. 2022. Virtual screening of Indonesian herbal compounds as COVID-19 supportive therapy: Machine learning and pharmacophore modeling approaches. BMC Complementary Med. Ther. 22(1):207. doi:10.1186/s12906- 022-03686-y.

Fan Y, Li X, Zhang L, Wan S, Zhang L, Zhou F. 2022. SARS-CoV-2 Omicron variant: Recent progress and future perspectives. Signal Transduction Targeted Ther. 7(1):141. doi:10.1038/s41392-022-00997-x.

Firdayani, Riswoko A, Helianti I. 2022. Inhibition of SARS-Cov-2 proteases by medicinal plant bioactive constituents: Molecular docking simulation. IOP Conf. Ser.: Earth Environ. Sci. 976(1):012054. doi:10.1088/1755-1315/976/1/012054.

Francis DM, Page R. 2010. Strategies to optimize protein expression in E. coli. Curr. Protoc. Protein Sci. 5(1):5.24.1–5.24.29. doi:10.1002/0471140864.ps0524s61.

Frederiksen LSF, Zhang Y, Foged C, Thakur A. 2020. The long road toward COVID-19 herd immunity: Vaccine platform technologies and mass immunization strategies. Front. Immunol. 11(July):1817. doi:10.3389/fimmu.2020.01817.

Freitas BT, Durie IA, Murray J, Longo JE, Miller HC, Crich D, Hogan RJ, Tripp RA, Pegan SD. 2020. Characterization and noncovalent inhibition of the deubiquitinase and deISGylase activity of SARS-CoV- 2 papain-like protease. ACS Infect. Dis. 6(8):2099– 2109. doi:10.1021/acsinfecdis.0c00168.

Fu H, Liang Y, Zhong X, Pan ZL, Huang L, Zhang HL, Xu Y, Zhou W, Liu Z. 2020. Codon optimization with deep learning to enhance protein expression. Sci. Rep. 10(1):1–9. doi:10.1038/s41598-020-74091-z.

Fu Z, Huang B, Tang J, Liu S, Liu M, Ye Y, Liu Z, Xiong Y, Zhu W, Cao D, Li J, Niu X, Zhou H, Zhao YJ, Zhang G, Huang H. 2021. The complex structure of GRL0617 and SARS-CoV-2 PLpro reveals a hot spot for antiviral drug discovery. Nat. Commun. 12(1):1– 12. doi:10.1038/s41467-020-20718-8.

Gao X, Qin B, Chen P, Zhu K, Hou P, Wojdyla JA, Wang M, Cui S. 2021. Crystal structure of SARS-CoV-2 papain-like protease. Acta Pharm. Sin. B 11(1):237– 245. doi:10.1016/j.apsb.2020.08.014.

Goldsmith CS, Tatti KM, Ksiazek TG, Rollin PE, Comer JA, Lee WW, Rota PA, Bankamp B, Bellini WJ, Zaki SR. 2004. Ultrastructural characterization of SARS Coronavirus. Emerging Infect. Dis. 10(2):320–326. doi:10.3201/eid1002.030913.

Hammond J, Leister-Tebbe H, Gardner A, Abreu P, Bao W, Wisemandle W, Baniecki M, Hendrick VM, Damle B, Simón-Campos A, Pypstra R, Rusnak JM. 2022. Oral nirmatrelvir for high-risk, nonhospitalized adults with COVID-19. New England Journal of Medicine 386(15):1397–1408. doi:10.1056/nejmoa2118542.

Hansen J, Baum A, Pascal KE, Russo V, Giordano S, Wloga E, Fulton BO, Yan Y, Koon K, Patel K, Chung KM, Hermann A, Ullman E, Cruz J, Rafique A, Huang T, Fairhurst J, Libertiny C, Malbec M, Lee WYY, Welsh R, Farr G, Pennington S, Deshpande D, Cheng J, Watty A, Bouffard P, Babb R, Levenkova N, Chen C, Zhang B, Romero Hernandez A, Saotome K, Zhou Y, Franklin M, Sivapalasingam S, Chien Lye D, Weston S, Logue J, Haupt R, Frieman M, Chen G, Olson W, Murphy AJ, Stahl N, Yancopoulos GD, Kyratsous CA, Hernandez AR, Saotome K, Zhou Y, Franklin M, Sivapalasingam S, Lye DC, Weston S, Logue J, Haupt R, Frieman M, Chen G, Olson W, Murphy AJ, Stahl N, Yancopoulos GD, Kyratsous CA. 2020. Studies in humanized mice and convalescent humans yield a SARS-CoV- 2 antibody cocktail. Science 369(6506):1010–1014. doi:10.1126/science.abd0827.

Hardison RL, Nelson SW, Barriga D, Ghere JM, Fenton GA, James RR, Stewart MJ, Lee SD, Calfee MW, Ryan SP, Howard MW. 2022. Efficacy of detergentbased cleaning methods against Coronavirus MHVA59 on porous and non-porous surfaces. Journal of Occupational and Environmental Hygiene 19(2):91– 101. doi:10.1080/15459624.2021.2015075.

Harrison AG, Lin T, Wang P. 2020. Mechanisms of SARS-CoV-2 transmission and pathogenesis. Trends Immunol. 41(12):1100–1115. doi:10.1016/

Hartenian E, Nandakumar D, Lari A, Ly M, Tucker JM, Glaunsinger BA. 2020. The molecular virology of coronaviruses. J. Biol. Chem. 295(37):12910–12934. doi:10.1074/jbc.REV120.013930.

Hu B, Guo H, Zhou P, Shi ZL. 2021. Characteristics of SARS-CoV-2 and COVID-19. Nat. Rev. Microbiol. 19(3):141–154. doi:10.1038/s41579-020-00459-7.

Hu T, Liu Y, Zhao M, Zhuang Q, Xu L, He Q. 2020. A comparison of COVID-19, SARS and MERS. PeerJ 8:1–30. doi:10.7717/peerj.9725.

Jackson CB, Farzan M, Chen B, Choe H. 2022. Mechanisms of SARS-CoV-2 entry into cells. Nat. Rev. Mol. Cell Biol. 23(1):3–20. doi:10.1038/s41580-021- 00418-x.

Janson JC. 2011. Principles, high resolution methods, and applications. Hoboken: Wiley, 3rd ed edition. Jeong K, Kim J, Chang JO, Hong S, Kim I, Oh S, Jeon S, Lee JC, Park HJ, Kim S, Lee W. 2022. Chemical screen uncovers novel structural classes of inhibitors of the papain-like protease of coronaviruses. iScience 25(10):105254. doi:10.1016/j.isci.2022.105254.

Jiang H, Yang P, Zhang J. 2022. Potential inhibitors targeting papain-like protease of SARS-CoV-2: Two birds with one stone. Front. Chem. 10(February):1–14. doi:10.3389/fchem.2022.822785.

Jungbauer A, Hahn R. 2009. Chapter 22 Ion-exchange chromatography. Methods Enzymol. 463:349–371. doi:10.1016/S0076-6879(09)63022-6.

Kabinger F, Stiller C, Schmitzová J, Dienemann C, Kokic G, Hillen HS, Höbartner C, Cramer P. 2021. Mechanism of molnupiravir-induced SARS-CoV-2 mutagenesis. Nat. Struct. Mol. Biol. 28(9):740–746. doi:10.1038/s41594-021-00651-0.

Kakodkar P, Kaka N, Baig M. 2020. A comprehensive literature review on the clinical presentation, and management of the pandemic Coronavirus disease 2019 (COVID-19). Cureus 12(4):e7560. doi:10.7759/cureus.7560.

Kayser O, Warzecha H. 2012. Pharmaceutical biotechnology: Drug discovery and clinical applications. Weinheim: Wiley-VCH, 2 edition. doi:10.1002/9783527632909.

Khow O, Suntrarachun S. 2012. Strategies for production of active eukaryotic proteins in bacterial expression system. Asian Pac. J. Trop. Biomed. 2(2):159–162. doi:10.1016/S2221-1691(11)60213-X.

Kim D, Lee JY, Yang JS, Kim JW, Kim VN, Chang H. 2020. The architecture of SARSCoV-2 transcriptome. Cell 181(4):914–921.e10. doi:10.1016/j.cell.2020.04.011.

Klemm T, Ebert G, Calleja DJ, Allison CC, Richardson LW, Bernardini JP, Lu BG, Kuchel NW, Grohmann C, Shibata Y, Gan ZY, Cooney JP, Doerflinger M, Au AE, Blackmore TR, Heden van Noort GJ, Geurink PP, Ovaa H, Newman J, RiboldiTunnicliffe A, Czabotar PE, Mitchell JP, Feltham R, Lechtenberg BC, Lowes KN, Dewson G, Pellegrini M, Lessene G, Komander D. 2020. Mechanism and inhibition of the papainlike protease, PLpro, of SARSCoV2. EMBO J. 39(18):e106275. doi:10.15252/embj.2020106275.

Kulandaisamy R, Kushwaha T, Dalal A, Kumar V, Singh D, Baswal K, Sharma P, Praneeth K, Jorwal P, Kayampeta SR, Sharma T, Maddur S, Kumar M, Kumar S, Polamarasetty A, Singh A, Sehgal D, Gholap SL, Appaiahgari MB, Katika MR, Inampudi KK. 2022. Repurposing of FDA approved drugs against SARS-CoV-2 papain-like protease: Computational, biochemical, and in vitro studies. Front. Microbiol. 13:877813. doi:10.3389/fmicb.2022.877813.

Kuo CJ, Chao TL, Kao HC, Tsai YM, Liu YK, Wang LH, Hsieh MC, Chang SY, Liang PH. 2021. Kinetic characterization and inhibitor screening for the proteases leading to identification of drugs against SARS-CoV- 2. Antimicrob. Agents Chemother. 65(4):e02577–20. doi:10.1128/AAC.02577-20.

Laksmiani NPL, Febryana Larasanty LP, Gde Jaya Santika AA, Andika Prayoga PA, Intan Kharisma Dewi AA, Ayu Kristiara Dewi NP. 2020. Active compounds activity from the medicinal plants against SARS-CoV-2 using in silico assay. Biomed. Pharmacol. J. 13(02):873–881. doi:10.13005/bpj/1953.

Lan J, Ge J, Yu J, Shan S, Zhou H, Fan S, Zhang Q, Shi X, Wang Q, Zhang L, Wang X. 2020. Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature 581(7807):215–220. doi:10.1038/s41586-020-2180-5.

Lee WS, Wheatley AK, Kent SJ, DeKosky BJ. 2020. Antibody-dependent enhancement and SARS-CoV-2 vaccines and therapies. Nat. Microbiol. 5(10):1185– 1191. doi:10.1038/s41564-020-00789-5.

Lim CT, Tan KW, Wu M, Ulferts R, Armstrong LA, Ozono E, Drury LS, Milligan JC, Zeisner TU, Zeng J, Weissmann F, Canal B, Bineva-Todd G, Howell M, O’Reilly N, Beale R, Kulathu Y, Labib K, Diffley JF. 2021. Identifying SARS-CoV-2 antiviral compounds by screening for small molecule inhibitors of Nsp3 papain-like protease. Biochem. J. 478(13):2517– 2531. doi:10.1042/BCJ20210244.

Lipinszki Z, Vernyik V, Farago N, Sari T, Puskas LG, Blattner FR, Posfai G, Gyorfy Z. 2018. Enhancing the translational capacity of E. coli by resolving the codon bias. ACS Synth. Biol. 7(11):2656–2664. doi:10.1021/acssynbio.8b00332.

Lozano Terol G, Gallego-Jara J, Sola Martínez RA, Martínez Vivancos A, Cánovas Díaz M, de Diego Puente T. 2021. Impact of the expression system on recombinant protein production in Escherichia coli BL21. Front. Microbiol. 12:682001. doi:10.3389/fmicb.2021.682001.

Lu R, Zhao X, Li J, Niu P, Yang B, Wu H, Wang W, Song H, Huang B, Zhu N, Bi Y, Ma X, Zhan F, Wang L, Hu T, Zhou H, Hu Z, Zhou W, Zhao L, Chen J, Meng Y, Wang J, Lin Y, Yuan J, Xie Z, Ma J, Liu WJ, Wang D, Xu W, Holmes EC, Gao GF, Wu G, Chen W, Shi W, Tan W. 2020. Genomic characterisation and epidemiology of 2019 novel coronavirus: Implications for virus origins and receptor binding. Lancet 395(10224):565–574. doi:10.1016/S0140- 6736(20)30251-8.

Luo Y, Zhao X, Zhou J, Yang J, Zhang Y, Kuang W, Peng J, Chen L, Zeng J. 2017. A network integration approach for drug-target interaction prediction and computational drug repositioning from heterogeneous information. Nat. Commun. 8(1). doi:10.1038/s41467- 017-00680-8.

Mantzourani C, Vasilakaki S, Gerogianni VE, Kokotos G. 2022. The discovery and development of transmembrane serine protease 2 (TMPRSS2) inhibitors as candidate drugs for the treatment of COVID- 19. Expert Opin. Drug Discovery 17(3):231–246. doi:10.1080/17460441.2022.2029843.

Mergulhão FJ, Summers DK, Monteiro GA. 2005. Recombinant protein secretion in Escherichia coli. Biotechnol. Adv. 23(3):177–202. doi:10.1016/j.biotechadv.2004.11.003.

Naqvi AAT, Fatima K, Mohammad T, Fatima U, Singh IK, Singh A, Atif SM, Hariprasad G, Hasan GM, Hassan MI. 2020. Insights into SARS-CoV-2 genome, structure, evolution, pathogenesis and therapies: Structural genomics approach. Biochim. Biophys. Acta, Mol. Basis Dis. 1866(10):165878. doi:10.1016/j.bbadis.2020.165878.

National Institute of Health (NIH). 2022. Antiviral agents, including antibody products. URL https://www.covid1

Ni W, Yang X, Yang D, Bao J, Li R, Xiao Y, Hou C, Wang H, Liu J, Yang D, Xu Y, Cao Z, Gao Z. 2020. Role of angiotensin-converting enzyme 2 (ACE2) in COVID- 19. Crit. Care 24(1):422. doi:10.1186/s13054-020- 03120-0.

Onyeaka H, Anumudu CK, Al-Sharify ZT, EgeleGodswill E, Mbaegbu P. 2021. COVID-19 pandemic: A review of the global lockdown and its far-reaching effects. Sci. Prog. 104(2):1–18. doi:10.1177/00368504211019854.

Osipiuk J, Azizi SA, Dvorkin S, Endres M, Jedrzejczak R, Jones KA, Kang S, Kathayat RS, Kim Y, Lisnyak VG, Maki SL, Nicolaescu V, Taylor CA, Tesar C, Zhang YA, Zhou Z, Randall G, Michalska K, Snyder SA, Dickinson BC, Joachimiak A. 2021. Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors. Nat. Commun. 12(1):743. doi:10.1038/s41467-021-21060-3.

Park JY, Kim JH, Kim YM, Jeong HJ, Kim DW, Park KH, Kwon HJ, Park SJ, Lee WS, Ryu YB. 2012. Tanshinones as selective and slow-binding inhibitors for SARS-CoV cysteine proteases. Bioorg. Med. Chem. 20(19):5928–5935. doi:10.1016/j.bmc.2012.07.038.

Patchett S, Lv Z, Rut W, Békés M, Drag M, Olsen SK, Huang TT. 2021. A molecular sensor determines the ubiquitin substrate specificity of SARS-CoV- 2 papain-like protease. Cell Rep. 36(13):109754. doi:10.1016/j.celrep.2021.109754.

Rando HM, MacLean AL, Lee AJ, Lordan R, Ray S, Bansal V, Skelly AN, Sell E, Dziak JJ, Shinholster L, McGowan LD, Guebila MB, Wellhausen N, Knyazev S, Boca SM, Capone S, Qi Y, Park Y, Mai D, Sun Y, Boerckel JD, Brueffer C, Byrd JB, Kamil JP, Wang J, Velazquez R, Szeto GL, Barton JP, Goel RR, Mangul S, Lubiana T, Gitter A, Greene CS. 2021. Pathogenesis, symptomatology, and transmission of SARS-CoV-2 through analysis of viral genomics and structure. mSystems 6(5):e00095–21. doi:10.1128/msystems.00095-21.

Razali R, Subbiah VK, Budiman C. 2021. Technical data of heterologous expression and purification of sarscov-2 proteases using Escherichia coli system. Data 6(9):99. doi:10.3390/data6090099.

Rizma BRP, Ananto AD, Sunarwidhi AL. 2021. The study of potential antiviral compounds from Indonesian medicinal plants as anti-COVID-19 with molecular docking approach. J. Mol. Docking 1(1):32–39. doi:10.33084/jmd.v1i1.2307.

Rosano GL, Ceccarelli EA. 2014. Recombinant protein expression in Escherichia coli: Advances and challenges. Front. Microbiol. 5:172. doi:10.3389/fmicb.2014.00172.

Rosano GL, Morales ES, Ceccarelli EA. 2019. New tools for recombinant protein production in Escherichia coli: A 5-year update. Protein Sci. 28(8):1412–1422. doi:10.1002/pro.3668.

Rosenberg ES, Dorabawila V, Easton D, Bauer UE, Kumar J, Hoen R, Hoefer D, Wu M, Lutterloh E, Conroy MB, Greene D, Zucker HA. 2022. Covid-19 vaccine effectiveness in New York State. N. Engl. J. Med. 386(2):116–127. doi:10.1056/nejmoa2116063.

Rudrapal M, Celik I, Chinnam S, Azam Ansari M, Khan J, Alghamdi S, Almehmadi M, Zothantluanga JH, Khairnar SJ. 2022. Phytocompounds as potential inhibitors of SARS-CoV-2 Mpro and PLpro through computational studies. Saudi J. Biol. Sci. 29(5):3456– 3465. doi:10.1016/j.sjbs.2022.02.028.

Rut W, Lv Z, Zmudzinski M, Patchett S, Nayak D, Snipas SJ, Oualid FE, Huang TT, Bekes M, Drag M, Olsen SK. 2020. Activity profiling and crystal structures of inhibitor-bound SARS-CoV-2 papain-like protease: A framework for anti–COVID-19 drug design. Sci. Adv. 6(42):1–13. doi:10.1126/sciadv.abd4596.

Ryu WS. 2017. Molecular Virology of Human Pathogenic Viruses. London: Elsevier. Sachs JD, Karim SSA, Aknin L, Allen J, Brosbøl K, Colombo F, Barron GC, Espinosa MF, Gaspar V, Gaviria A, Haines A, Hotez PJ, Koundouri P, Bascuñán FL, Lee JK, Pate MA, Ramos G, Reddy KS, Serageldin I, Thwaites J, Vike-Freiberga V, Wang C, Were MK, Xue L, Bahadur C, Bottazzi ME, Bullen C, Laryea-Adjei G, Ben Amor Y, Karadag O, Lafortune G, Torres E, Barredo L, Bartels JGE, Joshi N, Hellard M, Huynh UK, Khandelwal S, Lazarus JV, Michie S. 2022. The lancet commission on lessons for the future from the COVID-19 pandemic. Lancet 400(10359):1224–1280. doi:10.1016/S0140- 6736(22)01585-9.

Sanchez-Trincado JL, Gomez-Perosanz M, Reche PA. 2017. Fundamentals and methods for T- and B-cell epitope prediction. J. Immunol. Res. 2017:2680160. doi:10.1155/2017/2680160.

Schlegel S, Rujas E, Ytterberg AJ, Zubarev RA, Luirink J, de Gier JW. 2013. Optimizing heterologous protein production in the periplasm of E. coli by regulating gene expression levels. Microb. Cell Fact. 12(1):24. doi:10.1186/1475-2859-12-24.

Shen Z, Ratia K, Cooper L, Kong D, Lee H, Kwon Y, Li Y, Alqarni S, Huang F, Dubrovskyi O, Rong L, Thatcher GR, Xiong R. 2022. Design of SARS-CoV-2 PLpro inhibitors for COVID-19 antiviral therapy leveraging binding cooperativity. J. Med. Chem. 65(4):2940– 2955. doi:10.1021/acs.jmedchem.1c01307.

Shilling PJ, Mirzadeh K, Cumming AJ, Widesheim M, Köck Z, Daley DO. 2020. Improved designs for pET expression plasmids increase protein production yield in Escherichia coli. Commun. Biol. 3(1):24. doi:10.1038/s42003-020-0939-8.

Shin D, Mukherjee R, Grewe D, Bojkova D, Baek K, Bhattacharya A, Schulz L, Widera M, Mehdipour AR, Tascher G, Geurink PP, Wilhelm A, van der Heden van Noort GJ, Ovaa H, Müller S, Knobeloch KP, Rajalingam K, Schulman BA, Cinatl J, Hummer G, Ciesek S, Dikic I. 2020. Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. Nature 587(7835):657–662. doi:10.1038/s41586-020-2601-5.

Shirzad M, Nourigorji M, Sajedi A, Ranjbar M, Rasti F, Sourani Z, Moradi M, Mostafa Mir S, Memar MY. 2022. Targeted therapy in Coronavirus disease 2019 (COVID-19): Implication from cell and gene therapy to immunotherapy and vaccine. Int. Immunopharmacol. 111:109161. doi:10.1016/j.intimp.2022.109161.

Song JM, An YJ, Kang MH, Lee YH, Cha SS. 2012. Cultivation at 6-10 °C is an effective strategy to overcome the insolubility of recombinant proteins in Escherichia coli. Protein Expression and Purif. 82(2):297–301. doi:10.1016/j.pep.2012.01.020.

Tan H, Hu Y, Jadhav P, Tan B, Wang J. 2022. Progress and challenges in targeting the SARS-CoV-2 papainlike protease. J. Med. Chem. 65(11):7561–7580. doi:10.1021/acs.jmedchem.2c00303.

Taylor PC, Adams AC, Hufford MM, de la Torre I, Winthrop K, Gottlieb RL. 2021. Neutralizing monoclonal antibodies for treatment of COVID-19. Nat. Rev. Immunol. 21(6):382–393. doi:10.1038/s41577- 021-00542-x.

Thenawidjaja M, Ismaya WT, Retnoningrum DS. 2017. Protein - Serial Biokimia Mudah dan Menggugah [Protein - Easy and Intriguing Biochemistry Series]. Jakarta: PT. Grasindo.

Trowitzsch S, Bieniossek C, Nie Y, Garzoni F, Berger I. 2010. New baculovirus expression tools for recombinant protein complex production. J. Struct. Biol. 172(1):45–54. doi:10.1016/j.jsb.2010.02.010.

Ulfah M, Mulyawati L, Riswoko A, Helianti I. 2022. Expression of recombinant SARS-CoV-2 papain-like protease (SARS-CoV-2 PLpro) in Escherichia coli RIPL. IOP Conf. Ser.: Earth Environ. Sci. 976(1):1– 10. doi:10.1088/1755-1315/976/1/012033.

Wang C, Horby PW, Hayden FG, Gao GF. 2020. A novel coronavirus outbreak of global health concern. Lancet 395(10223):470–473. doi:10.1016/S0140-6736(20)30185-9.

Wang H, Wang F, Wang W, Yao X, Wei D, Cheng H, Deng Z. 2014. Improving the expression of recombinant proteins in E. coli BL21 (DE3) under acetate stress: An alkaline ph shift approach. PLoS ONE 9(11):e112777. doi:10.1371/journal.pone.0112777.

Waugh DS. 2011. An overview of enzymatic reagents for the removal of affinity tags. Protein Expression Purif. 80(2):283–293. doi:10.1016/j.pep.2011.08.005.

WHO. 2023. WHO Coronavirus (COVID-19) Dashboard. World Health Organization. URL https://covid19.wh

Wu C, Liu Y, Yang Y, Zhang P, Zhong W, Wang Y, Wang Q, Xu Y, Li M, Li X, Zheng M, Chen L, Li H. 2020. Analysis of therapeutic targets for SARSCoV-2 and discovery of potential drugs by computational methods. Acta Pharm. Sin. B 10(5):766–788. doi:10.1016/j.apsb.2020.02.008.

Xu Y, Chen K, Pan J, Lei Y, Zhang D, Fang L, Tang J, Chen X, Ma Y, Zheng Y, Zhang B, Zhou Y, Zhan J, Xu W. 2021. Repurposing clinically approved drugs for COVID-19 treatment targeting SARS-CoV-2 papain-like protease. Int. J. Biol. Macromol. 188(January):137–146. doi:10.1016/j.ijbiomac.2021.07.184.

Yang Y, Xiao Z, Ye K, He X, Sun B, Qin Z, Yu J, Yao J, Wu Q, Bao Z, Zhao W. 2020. SARS-CoV-2: characteristics and current advances in research. Virol. J. 17(1):1–17. doi:10.1186/s12985-020-01369-z.

Yao H, Song Y, Chen Y, Wu N, Xu J, Sun C, Zhang J, Weng T, Zhang Z, Wu Z, Cheng L, Shi D, Lu X, Lei J, Crispin M, Shi Y, Li L, Li S. 2020. Molecular architecture of the SARS-CoV-2 virus. Cell 183(3):730– 738.e13. doi:10.1016/j.cell.2020.09.018.

Yi Y, Zhang M, Xue H, Yu R, Bao YO, Kuang Y, Chai Y, Ma W, Wang J, Shi X, Li W, Hong W, Li J, Muturi E, Wei H, Wlodarz J, Roszak S, Qiao X, Yang H, Ye M. 2022. Schaftoside inhibits 3CLpro and PLpro of SARS-CoV-2 virus and regulates immune response and inflammation of host cells for the treatment of COVID-19. Acta Pharm. Sin. B 12(11):4154–4164. doi:10.1016/j.apsb.2022.07.017.

Yu W, Zhao Y, Ye H, Wu N, Liao Y, Chen N, Li Z, Wan N, Hao H, Yan H, Xiao Y, Lai M. 2022. Structure-based design of a dual-targeted covalent inhibitor against papain-like and main proteases of SARS-CoV-2. J. Med. Chem. 65(24):16252–16267. doi:10.1021/acs.jmedchem.2c00954.

Zeng W, Liu G, Ma H, Zhao D, Yang Y, Liu M, Mohammed A, Zhao C, Yang Y, Xie J, Ding C, Ma X, Weng J, Gao Y, He H, Jin T. 2020. Biochemical characterization of SARS-CoV-2 nucleocapsid protein. Biochem. Biophys. Res. Commun. 527(3):618– 623. doi:10.1016/j.bbrc.2020.04.136.

Zhang Z, Nomura N, Muramoto Y, Ekimoto T, Uemura T, Liu K, Yui M, Kono N, Aoki J, Ikeguchi M, Noda T, Iwata S, Ohto U, Shimizu T. 2022. Structure of SARSCoV-2 membrane protein essential for virus assembly. Nat. Commun. 13(1):1–7. doi:10.1038/s41467-022- 32019-3.

Zhao Y, Du X, Duan Y, Pan X, Sun Y, You T, Han L, Jin Z, Shang W, Yu J, Guo H, Liu Q, Wu Y, Peng C, Wang J, Zhu C, Yang X, Yang K, Lei Y, Guddat LW, Xu W, Xiao G, Sun L, Zhang L, Rao Z, Yang H. 2021. High-throughput screening identifies established drugs as SARS-CoV-2 PLpro inhibitors. Protein Cell 12(11):877–888. doi:10.1007/s13238-021- 00836-9.

Zheng J. 2020. SARS-coV-2: An emerging coronavirus that causes a global threat. Int. J. Biol. Sci. 16(10):1678–1685. doi:10.7150/ijbs.45053.

Zhou YW, Xie Y, Tang LS, Pu D, Zhu YJ, Liu JY, Ma XL. 2021. Therapeutic targets and interventional strategies in COVID-19: mechanisms and clinical studies. Signal Transduction Targeted Ther. 6(1):317. doi:10.1038/s41392-021-00733-x.


Article Metrics

Abstract views : 725 | views : 624


  • There are currently no refbacks.

Copyright (c) 2023 The Author(s)

Creative Commons License
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.