The current state of validated small molecules inhibiting SARS-CoV-2 nonstructural proteins
The current state of validated small molecules inhibiting SARS-CoV-2 nonstructural proteins
The current COVID-19 outbreak has had a profound influence on public health and daily life. Despite all restrictions and vaccination programs, COVID-19 still can lead to fatality due to a lack of COVID-19-specific treatments. A number of studies have demonstrated the feasibility to develop therapeutics by targeting underlying components of the viral proteome. Here we reviewed recently developed and validated small molecule inhibitors of SARS-CoV-2’s nonstructural proteins. We described the validation level of identified compounds specific for SARS-CoV-2 in the presence of in vitro and in vivo supporting data. The mechanisms of pharmacological activity, as well as approaches for developing improved SARS-CoV-2 NSP inhibitors have been emphasized.
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- Agostini ML, Pruijssers AJ, Chappell JD, Gribble J, Lu X et al. (2019). Small-molecule antiviral β-d-N4-hydroxycytidine inhibits a proofreading-intact coronavirus with a high genetic barrier to resistance. Journal of Virology 93.
- Angelini MM, Akhlaghpour M, Neuman BW, Buchmeier MJ, Moscona A (2013). Severe acute respiratory syndrome coronavirus nonstructural proteins 3, 4, and 6 induce doublemembrane vesicles. mBio 4.
- Azkur AK, Akdis M, Azkur D, Sokolowska M, Veen W et al. (2020). Immune response to SARS‐CoV‐2 and mechanisms of immunopathological changes in COVID‐19. Allergy 75: 1564- 1581.
- Báez-Santos YM, St. John SE, Mesecar AD (2015). The SARScoronavirus papain-like protease: structure, function and inhibition by designed antiviral compounds. Antiviral Research 115: 21-38.
- Basier C, Basu S, Beale R, Canal B, Cowling VH et al. (2021). Identification of SARS-CoV-2 antiviral compounds by screening for small molecule inhibitors of the nsp14 RNA cap methyltransferase. bioRxiv.
- Bulut C, Kato Y (2020). Epidemiology of COVID-19. Turkish Journal of Medical Sciences 50: 563-570.
- Canal B, McClure AW, Curran JF, Wu M, Ulferts R et al. (2021). Identifying SARS-CoV-2 antiviral compounds by screening for small molecule inhibitors of Nsp14/nsp10 exoribonuclease. bioRxiv 2021.2004.2007.438812
- Chang L-J, Chen T-H (2021). NSP16 2′-O-MTase in coronavirus pathogenesis: possible prevention and treatments strategies. Viruses 13: 538.
- Chen Y, Su C, Ke M, Jin X, Xu L et al. (2011). Biochemical and structural insights into the mechanisms of SARS coronavirus RNA ribose 2′-O-methylation by nsp16/nsp10 protein complex. PLoS Pathog 7: e1002294.
- Chien M, Anderson TK, Jockusch S, Tao C, Li X et al. (2020). Nucleotide analogues as inhibitors of SARS-CoV-2 Polymerase, a key drug target for COVID-19. Journal of Proteome Research 19: 4690-4697.
- Clark LK, Green TJ, Petit CM, Dutch RE (2021). Structure of nonstructural protein 1 from SARS-CoV-2. Journal of Virology 95.
- Coelho C, Gallo G, Campos CB, Hardy L, Würtele M (2020). Biochemical screening for SARS-CoV-2 main protease inhibitors. PloS one 15: e0240079.
- Cornillez-Ty CT, Liao L, Yates JR, Kuhn P, Buchmeier MJ (2009). Severe acute respiratory syndrome coronavirus nonstructural protein 2 interacts with a host protein complex involved in mitochondrial biogenesis and intracellular signaling. Journal of Virology 83: 10314-10318.
- Cottam EM, Maier HJ, Manifava M, Vaux LC, ChandraSchoenfelder P et al. (2011). Coronavirus nsp6 proteins generate autophagosomes from the endoplasmic reticulum via an omegasome intermediate. Autophagy 7: 1335-1347.
- Cottam EM, Whelband MC, Wileman T (2014). Coronavirus NSP6 restricts autophagosome expansion. Autophagy 10: 1426-1441.
- Dai W, Zhang B, Jiang X-M, Su H, Li J et al. (2020). Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease. Science 368: 1331-1335.
- Decroly E, Debarnot C, Ferron F, Bouvet M, Coutard B et al. (2011). Crystal structure and functional analysis of the SARScoronavirus RNA cap 2′-O-methyltransferase nsp10/nsp16 complex. PLoS Pathog 7: e1002059.
- Den Boon JA, Ahlquist P (2010). Organelle-like membrane compartmentalization of positive-strand RNA virus replication factories. Annual Review of Microbiology 64: 241-256.
- Farias AB, Candiotto G, Siragusa L, Goracci L, Cruciani G et al. (2021). Targeting Nsp9 as an anti-SARS-CoV-2 strategy. New Journal of Chemistry 45: 522-525.
- Freitas BT, Durie IA, Murray J, Longo JE, Miller HC et al. (2020). Characterization and noncovalent inhibition of the deubiquitinase and deISGylase activity of SARS-CoV-2 papain-like protease. ACS Infectious Diseases 6: 2099-2109.
- Gadhave K, Kumar P, Kumar A, Bhardwaj T, Garg N et al. (2020). NSP 11 of SARS-CoV-2 is an intrinsically disordered protein. bioRxiv
- Gadhave K, Kumar P, Kumar A, Bhardwaj T, Garg N et al. (2021). Conformational dynamics of 13 amino acids long NSP11 of SARS-CoV-2 under membrane mimetics and different solvent conditions. Microbial Pathogenesis 105041
- Gao Y, Yan L, Huang Y, Liu F, Zhao Y et al. (2020). Structure of the RNA-dependent RNA polymerase from COVID-19 virus. Science 368: 779-782.
- Glaab E, Manoharan GB, Abankwa D (2021). A pharmacophore model for SARS-CoV-2 3CLpro small molecule inhibitors and in vitro experimental validation of computationally screened inhibitors. bioRxiv.
- Goldsmith CS, Tatti KM, Ksiazek TG, Rollin PE, Comer JA et al. (2004). Ultrastructural characterization of SARS coronavirus. Emerging Infectious Diseases 10: 320-326.
- Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K et al. (2020). A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature 583: 459-468.
- Greig SL (2016). Sofosbuvir/velpatasvir: a review in chronic hepatitis C. Drugs 76: 1567-1578.
- Griffin JWD (2020). SARS-CoV and SARS-CoV-2 main protease residue interaction networks change when bound to inhibitor N3. Journal of Structural Biology 211: 107575.
- Güler G, Özdemir H, Omar D, Akdoğan G (2021). Coronavirus disease 2019 (COVID-19): Biophysical and biochemical aspects of SARS-CoV-2 and general characteristics. Progress in Biophysics and Molecular Biology.
- Gupta M, Azumaya CM, Moritz M, Pourmal S, Diallo A et al. (2021). CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes. bioRxiv. Hagemeijer M, Rottier P, Haan C (2012). Biogenesis and dynamics of the coronavirus replicative structures. Viruses 4: 3245-3269.
- Hasöksüz M, Kiliç S, Saraç F (2020). Coronaviruses and SARSCOV-2. Turkish Journal of Medical Sciences 50: 549-556.
- Hoffmann HH, Sánchez-Rivera FJ, Schneider WM, Luna JM, SotoFeliciano YM et al. (2021). Functional interrogation of a SARSCoV-2 host protein interactome identifies unique and shared coronavirus host factors. Cell Host & Microbe 29: 267-280. e265.
- Iketani S, Forouhar F, Liu H, Hong SJ, Lin F-Y et al. (2021). Lead compounds for the development of SARS-CoV-2 3CL protease inhibitors. Nature Communications 12.
- Imbert I, Guillemot JC, Bourhis JM, Bussetta C, Coutard B et al. (2006). A second, non-canonical RNA-dependent RNA polymerase in SARS Coronavirus. The EMBO Journal 25: 4933-4942.
- Jena AB, Kanungo N, Nayak V, Chainy GBN, Dandapat J (2021). Author correction: catechin and curcumin interact with S protein of SARS-CoV2 and ACE2 of human cell membrane: insights from computational studies. Scientific reports 11.
- Jin Z, Du X, Xu Y, Deng Y, Liu M, Zhao Y, Zhang B et al. (2020). Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors. Nature 582: 289-293.
- Jin Z, Zhao Y, Sun Y, Zhang B, Wang H et al. (2020). Structural basis for the inhibition of SARS-CoV-2 main protease by antineoplastic drug carmofur. Nature Structural & Molecular Biology 27: 529-532.
- Kasprzyk R, Spiewla TJ, Golojuch S, Vangeel L, Jonghe SD et al. (2021). Identification and evaluation of potential SARSCoV-2 antiviral agents targeting mRNA cap guanine N7- methyltransferase. Antiviral Research 193: 105142.
- Khalili Yazdi A, Li F, Devkota K, Perveen S, Ghiabi P et al. (2021). A high-throughput radioactivity-based assay for screening SARS-CoV-2 nsp10-nsp16 complex. SLAS DISCOVERY: Advancing the Science of Drug Discovery 26: 757-765.
- Kim N-E, Kim D-K, Song Y-J (2021). SARS-CoV-2 nonstructural proteins 1 and 13 suppress caspase-1 and the NLRP3 inflammasome activation. Microorganisms 9: 494.
- Kim Y, Jedrzejczak R, Maltseva NI, Wilamowski M, Endres M et al. (2020). Crystal structure of Nsp15 endoribonuclease NendoU from SARS‐CoV‐2. Protein Science 29: 1596-1605.
- Kim Y, Jedrzejczak R, Maltseva NI, Wilamowski M, Endres M et al. (2020). Crystal structure of Nsp15 endoribonuclease NendoU from SARS‐CoV‐2. Protein Science 29: 1596-1605.
- Kim Y, Wower J, Maltseva N, Chang C, Jedrzejczak R et al. (2021). Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2. Communications Biology 4.
- Klemm T, Ebert G, Calleja DJ, Allison CC, Richardson LW et al. (2020). Mechanism and inhibition of the papain‐like protease, PLpro, of SARS‐CoV‐2. The EMBO Journal 39.
- Kocabas F, Aslan GS (2015). Fluorometric CCHFV OTU protease assay with potent inhibitors. Virus Genes 51: 190-197.
- Kocabaş F, Ergin EK (2016). Identification of small molecule binding pocket for inhibition of Crimean–Congo hemorrhagic fever virus OTU protease. Turkish Journal of Biology 40: 239-249.
- Kocabas F, Turan RD, Aslan GS (2015). Fluorometric RdRp assay with self-priming RNA. Virus genes 50: 498-504.
- Kokic G, Hillen HS, Tegunov D, Dienemann C, Seitz F et al. (2021). Mechanism of SARS-CoV-2 polymerase stalling by remdesivir. Nature Communications 12.
- Kuo C-J, Chao T-L, Kao H-C, Tsai Y-M, Liu Y-K et al. (2021). Kinetic characterization and Inhibitor Screening for the Proteases Leading to Identification of Drugs against SARS-CoV-2. Antimicrobial Agents and chemotherapy 65:
- Levine B (2005). Eating oneself and uninvited guests. Cell 120: 159- 162.
- Lin S, Chen H, Ye F, Chen Z, Yang F et al. (2020). Crystal structure of SARS-CoV-2 nsp10/nsp16 2′-O-methylase and its implication on antiviral drug design. Signal Transduction and Targeted Therapy 5: 1-4.
- Littler DR, Gully BS, Colson RN, Rossjohn J (2020). Crystal structure of the SARS-CoV-2 non-structural protein 9, Nsp9. Iscience 23: 101258.
- Liu C, Boland S, Scholle MD, Bardiot D, Marchand A et al. (2021). Dual inhibition of SARS-CoV-2 and human rhinovirus with protease inhibitors in clinical development. Antiviral Research 187: 105020.
- Lu G, Zhang X, Zheng W, Sun J, Hua L, Xu L et al. (2020). Development of a simple in vitro assay to identify and evaluate nucleotide analogs against SARS-CoV-2 RNA-dependent RNA polymerase. Antimicrobial Agents and Chemotherapy 65.
- Ma C, Sacco MD, Hurst B, Townsend JA, Hu Y et al. (2020). Boceprevir, GC-376, and calpain inhibitors II, XII inhibit SARS-CoV-2 viral replication by targeting the viral main protease. Cell Research 30: 678-692.
- Maio N, Lafont BAP, Sil D, Li Y, Bollinger JM et al. (2021). Fe-S cofactors in the SARS-CoV-2 RNA-dependent RNA polymerase are potential antiviral targets. Science eabi5224 Mali SN (2020). The rise of new coronavirus infection-(COVID-19): a recent update. Eurasian Journal of Medicine and Oncology .
- Matsuyama S, Kawase M, Nao N, Shirato K, Ujike M et al. (2020). The Inhaled steroid ciclesonide blocks SARS-CoV-2 RNA replication by targeting the viral replication-transcription complex in cultured cells. Journal of Virology 95 (1): e01648- 20. doi: 10.1128/JVI.01648-20.
- McClain CB, Vabret N (2020). SARS-CoV-2: the many pros of targeting PLpro. Signal Transduction and Targeted Therapy 5. Mengist HM, Dilnessa T, Jin T (2021). Structural basis of potential inhibitors targeting SARS-CoV-2 main protease. Frontiers in Chemistry 9.
- Mengist HM, Fan X, Jin T (2020). Designing of improved drugs for COVID-19: crystal structure of SARS-CoV-2 main protease Mpro. Signal Transduction and Targeted Therapy 5.
- Mutlu O, Ugurel OM, Sariyer E, Ata O, Inci TG et al. (2020). Targeting SARS-CoV-2 Nsp12/Nsp8 interaction interface with approved and investigational drugs: an in silico structurebased approach. Journal of Biomolecular Structure and Dynamics 1-13.
- Naydenova K, Muir KW, Wu L-F, Zhang Z, Coscia F et al. (2021). Structure of the SARS-CoV-2 RNA-dependent RNA polymerase in the presence of favipiravir-RTP. Proceedings of the National Academy of Sciences 118: e2021946118.
- Osipiuk J, Azizi S-A, Dvorkin S, Endres M, Jedrzejczak R et al. (2021). Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors. Nature communications 12:1-9
- Pandey P, Prasad K, Prakash A, Kumar V (2020). Insights into the biased activity of dextromethorphan and haloperidol towards SARS-CoV-2 NSP6: in silico binding mechanistic analysis. Journal of Molecular Medicine 98: 1659-1673.
- Paul AV, Wimmer E (2015). Initiation of protein-primed picornavirus RNA synthesis. Virus Research 206: 12-26.
- Peng Q, Peng R, Yuan B, Zhao J, Wang M et al. (2020). Structural and biochemical characterization of the nsp12-nsp7-nsp8 core polymerase complex from SARS-CoV-2. Cell Reports 31: 107774.
- Perveen S, Khalili Yazdi A, Devkota K, Li F, Ghiabi P et al. (2021). A high-throughput RNA displacement assay for screening SARSCoV-2 nsp10-nsp16 complex toward developing therapeutics for COVID-19. SLAS DISCOVERY: sdvancing the Science of Drug Discovery 26: 620-627.
- Petrosillo N, Viceconte G, Ergonul O, Ippolito G, Petersen E (2020). COVID-19, SARS and MERS: are they closely related? Clinical Microbiology and Infection 26: 729-734.
- Pitsillou E, Liang J, Ververis K, Lim KW, Hung A et al. (2020). Identification of Small molecule inhibitors of the deubiquitinating activity of the SARS-CoV-2 papain-like protease: in silico molecular docking studies and in vitro enzymatic activity assay. Frontiers in Chemistry 8.
- Pruijssers AJ, Denison MR (2019). Nucleoside analogues for the treatment of coronavirus infections. Current Opinion in Virology 35: 57-62.
- Qiao J, Li Y-S, Zeng R, Liu F-L, Luo R-H et al. (2021). SARS-CoV-2 Mpro inhibitors with antiviral activity in a transgenic mouse model. Science 371: 1374-1378.
- Rathnayake AD, Zheng J, Kim Y, Perera KD, Mackin S et al. (2020). 3C-like protease inhibitors block coronavirus replication in vitro and improve survival in MERS-CoV–infected mice. Science Translational Medicine 12: eabc5332.
- Ratia K, Saikatendu KS, Santarsiero BD, Barretto N, Baker SC et al. (2006). Severe acute respiratory syndrome coronavirus papainlike protease: structure of a viral deubiquitinating enzyme. Proceedings of the National Academy of Sciences 103: 5717- 5722.
- Riva L, Yuan S, Yin X, Martin-Sancho L, Matsunaga N et al. (2020). A Large-scale Drug Repositioning Survey for SARS-CoV-2 Antivirals. bioRxiv.
- Riva L, Yuan S, Yin X, Martin-Sancho L, Matsunaga N et al. (2020). Discovery of SARS-CoV-2 antiviral drugs through large-scale compound repurposing. Nature 586: 113-119.
- Rodriguez-Torres M, Lawitz E, Kowdley KV, Nelson DR, DeJesus E et al. (2013). Sofosbuvir (GS-7977) plus peginterferon/ ribavirin in treatment-naïve patients with HCV genotype 1: a randomized, 28-day, dose-ranging trial. Journal of Hepatology 58: 663-668.
- Sakai Y, Kawachi K, Terada Y, Omori H, Matsuura Y et al. (2017). Two-amino acids change in the nsp4 of SARS coronavirus abolishes viral replication. Virology 510: 165-174.
- Schoggins JW, Rice CM (2011). Interferon-stimulated genes and their antiviral effector functions. Current Opinion in Virology 1: 519-525.
- Sharma M, Prasher P, Mehta M, Zacconi FC, Singh Y et al. (2020). Probing 3CL protease: rationally designed chemical moieties for COVID‐19. Drug Development Research 81: 911-918.
- Sharun K, Tiwari R, Dhama K (2021). Protease inhibitor GC376 for COVID-19: lessons learned from feline infectious peritonitis. Annals of Medicine and Surgery 61: 122-125.
- Sheahan TP, Sims AC, Zhou S, Graham RL, Hill CS et al. (2020). An orally bioavailable broad-spectrum antiviral inhibits SARSCoV-2 and multiple endemic, epidemic and bat coronavirus. bioRxiv 2020. 2003.2019.997890
- Sheahan TP, Sims AC, Zhou S, Graham RL, Pruijssers AJ et al. (2020). An orally bioavailable broad-spectrum antiviral inhibits SARSCoV-2 in human airway epithelial cell cultures and multiple coronaviruses in mice. Science Translational Medicine 12: eabb5883.
- Shin D, Mukherjee R, Grewe D, Bojkova D, Baek K et al. (2020). Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. Nature 587: 657-662.
- Sies H, Parnham MJ (2020). Potential therapeutic use of ebselen for COVID-19 and other respiratory viral infections. Free Radical Biology and Medicine 156: 107-112.
- Su H, Yao S, Zhao W, Li M, Liu J et al. (2020). Discovery of baicalin and baicalein as novel, natural product inhibitors of SARSCoV-2 3CL protease in vitro. BioRxiv.
- Subissi L, Imbert I, Ferron F, Collet A, Coutard B et al. (2014a). SARS-CoV ORF1b-encoded nonstructural proteins 12–16: replicative enzymes as antiviral targets. Antiviral Research 101: 122-130.
- Subissi L, Posthuma CC, Collet A, Zevenhoven-Dobbe JC, Gorbalenya AE et al. (2014b). One severe acute respiratory syndrome coronavirus protein complex integrates processive RNA polymerase and exonuclease activities. Proceedings of the National Academy of Sciences 111: E3900-E3909.
- Suryawanshi RK, Koganti R, Agelidis A, Patil CD, Shukla D (2021). Dysregulation of cell signaling by SARS-CoV-2. Trends in Microbiology 29: 224-237.
- Taştan C, Yurtsever B, Sir Karakuş G, Dilek Kançağı D, Demir S et al. (2020). SARS-CoV-2 isolation and propagation from Turkish COVID-19 patients. Turkish Journal of Biology 44: 192-202. Te Velthuis AJW, Van Den Worm SHE, Snijder EJ (2012). The SARScoronavirus nsp7+nsp8 complex is a unique multimeric RNA polymerase capable of both de novo initiation and primer extension. Nucleic Acids Research 40:1737-1747
- Tidu A, Janvier A, Schaeffer L, Sosnowski P, Kuhn L et al. (2021). The viral protein NSP1 acts as a ribosome gatekeeper for shutting down host translation and fostering SARS-CoV-2 translation. Rna 27: 253-264.
- Ullrich S, Nitsche C (2020). The SARS-CoV-2 main protease as drug target. Bioorganic & Medicinal Chemistry Letters 30: 127377. van Dijk AA, Makeyev EV, Bamford DH (2004). Initiation of viral RNA-dependent RNA polymerization. Journal of General Virology 85: 1077-1093.
- Vuong W, Fischer C, Khan MB, Van Belkum MJ, Lamer T et al. (2021). Improved SARS-CoV-2 Mpro inhibitors based on feline antiviral drug GC376: structural enhancements, increased solubility, and micellar studies. European Journal of Medicinal Chemistry 222:113584
- Vuong W, Khan MB, Fischer C, Arutyunova E, Lamer T et al. (2020). Feline coronavirus drug inhibits the main protease of SARSCoV-2 and blocks virus replication. Nature Communications 11.
- Wang C-W, Klionsky DJ (2003). The molecular mechanism of autophagy. Molecular Medicine 9: 65-76.
- Wang M, Cao R, Zhang L, Yang X, Liu J et al. (2020). Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Research 30: 269-271.
- Wang Q, Wu J, Wang H, Gao Y, Liu Q et al. (2020). Structural basis for RNA replication by the SARS-CoV-2 polymerase. Cell 182: 417-428. e413.
- Wang Y, Lv Z, Chu Y (2015). HIV protease inhibitors: a review of molecular selectivity and toxicity. HIV/AIDS - Research and Palliative Care 95.
- Warren TK, Wells J, Panchal RG, Stuthman KS, Garza NL et al. (2014). Protection against filovirus diseases by a novel broadspectrum nucleoside analogue BCX4430. Nature 508: 402-405.
- White MA, Lin W, Cheng X (2020). Discovery of COVID-19 inhibitors targeting the SARS-CoV-2 Nsp13 helicase. The Journal of Physical Chemistry Letters 11: 9144-9151.
- Xie M, Chen Q (2020). Insight into 2019 novel coronavirus — an updated interim review and lessons from SARS-CoV and MERS-CoV. International Journal of Infectious Diseases 94: 119-124.
- Yoshimoto FK (2020). The proteins of severe acute respiratory syndrome coronavirus-2 (SARS CoV-2 or n-COV19), the cause of COVID-19. The Protein Journal 39: 198-216.
- Ysrafil Y, Astuti I, Mus R, Gama NI, Rahmaisyah D et al. (2020). A summary of coronavirus disease 2019: what we should know? Pharmaceutical Sciences 26: S24-S35.
- Yuen C-K, Lam J-Y, Wong W-M, Mak L-F, Wang X et al. (2020). SARS-CoV-2 nsp13, nsp14, nsp15 and orf6 function as potent interferon antagonists. Emerging Microbes & Infections 9: 1418-1428.
- Zhang C-h, Wang Y-f, Liu X-j, Lu J-H, Qian C-w et al. (2005). Antiviral activity of cepharanthine against severe acute respiratory syndrome coronavirus in vitro. Chinese medical journal 118: 493-496.
- Zhang L, Lin D, Sun X, Curth U, Drosten C et al. (2020). Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors. Science 368: 409- 412.
- Zhu W, Shyr ZA, Lo DC, Zheng W (2021). Viral proteases as targets for COVID-19 drug development. Journal of Pharmacology and Experimental Therapeutics JPET-MR-2021-000688