CoV Replicase polyprotein 1ab

Target id: 3125

Nomenclature: CoV Replicase polyprotein 1ab

Database Links
ChEMBL Target	CHEMBL4523582 (SARS-CoV-2), CHEMBL5118 (SARS-CoV)
UniProtKB	P0DTD1 (SARS-CoV-2), P0C6X7 (SARS-CoV)

General Comments
The pp1ab polyprotein is a pro-protein, that is proteolytically cleaved to form 16 shorter proteins. The first 11 proteins are also cleaved from pp1a. Nsps 12-16 are unique to pp1ab [18]. Most of what is predicted about the functions of these proteins is implied by similarities to orthologues from other coronaviruses [5-6]. Non-structural protein 12 behaves as a RNA-dependent RNA polymerase (RdRp) that copies the viral RNA template [2]. This is the molecular target of nucleotide analogue antiviral drugs like remdesivir, tenofovir and ribavirin [7,17]. It has a zinc-binding domain in its N-terminus and its activity is magnesium-dependent [1,8,15]. Cryo-EM resolution of the SARS-CoV-2 polymerase complex architecture shows that it contains the nsp12 catalytic subunit and nsp7-nsp8 co-factors [10]. Experimental evidence reveals that nsp12 antagonises the host antiviral type I interferon response to SARS-CoV-2 infection by suppresseing nuclear translocation of IRF3 [16]. Non-structural protein 13 has helicase unwinding activity. Small molecule inhibitors of MERS-CoV helicase have been reported [19]. There is a report of a novel allosteric nsp13 inhibitor that was designed for SARS-CoV-2 antiviral potential [12]. Non-structural protein 14 is a manganese-dependent uridylate-specific endoribonuclease with proofreading exoribonuclease activity that is required for fidelity during viral RNA synthesis. A nsp10/nsp14 complex exerts potent exoribonuclease activity that may be connected to a replicative mismatch repair mechanism [4]. The presence of nsp14 is predicted to be responsible for the high resistance of coronaviruses to many nucleoside analogue inhibitors [11]. Non-structural protein 15 (NendoU) is a uridylate-specific endoribonuclease [20]. The catalytic activity of MERS-CoV nsp15 can be modulated by interactions with other nsps (e.g. nsp8 and a nsp7/8 complex), oligomeric assembly and RNA binding efficiency. Nsp15 is essential in coronavirus biology, but interestingly its deletion does not disrupt replication, so its principal action remains elusive. A resolved X-ray structure has been published and deposited with the RCSB Protein Data Bank (6W01) [9]. This shows that enzymatic functional arises from a hexameric complex whose similarity to SARS-CoV nsp15 suggests that inhibitors of this older coronavirus may also inhibit the more recently identified one. MERS-CoV nsp15 inhibitors are considered to be unlikely to inhibit SARS-CoV-2 nsp15. Non-structural protein 16 dimerises with nsp10 to form a 2'-O-methyltransferase that mediates 2'-O-ribose methylation to the 5'-cap structure of viral mRNAs [3], and this activity helps to improve viral protein translation, to limit host immune detection and inhibit the host's anti-viral interferon response [14]. High-resolution structures of the SARS-CoV-2 nsp16/10 heterodimer have been reported (see for example PDB ID 6W4H) [13]. Such analysis reveals any domains that could be exploited for the development of antiviral inhibitors, which could act to either prevent substrate interaction or block heterodimer formation.

The pp1ab polyprotein is a pro-protein, that is proteolytically cleaved to form 16 shorter proteins. The first 11 proteins are also cleaved from pp1a. Nsps 12-16 are unique to pp1ab [18]. Most of what is predicted about the functions of these proteins is implied by similarities to orthologues from other coronaviruses [5-6].

Non-structural protein 12 behaves as a RNA-dependent RNA polymerase (RdRp) that copies the viral RNA template [2]. This is the molecular target of nucleotide analogue antiviral drugs like remdesivir, tenofovir and ribavirin [7,17]. It has a zinc-binding domain in its N-terminus and its activity is magnesium-dependent [1,8,15]. Cryo-EM resolution of the SARS-CoV-2 polymerase complex architecture shows that it contains the nsp12 catalytic subunit and nsp7-nsp8 co-factors [10]. Experimental evidence reveals that nsp12 antagonises the host antiviral type I interferon response to SARS-CoV-2 infection by suppresseing nuclear translocation of IRF3 [16].

Non-structural protein 13 has helicase unwinding activity. Small molecule inhibitors of MERS-CoV helicase have been reported [19]. There is a report of a novel allosteric nsp13 inhibitor that was designed for SARS-CoV-2 antiviral potential [12].

Non-structural protein 14 is a manganese-dependent uridylate-specific endoribonuclease with proofreading exoribonuclease activity that is required for fidelity during viral RNA synthesis. A nsp10/nsp14 complex exerts potent exoribonuclease activity that may be connected to a replicative mismatch repair mechanism [4]. The presence of nsp14 is predicted to be responsible for the high resistance of coronaviruses to many nucleoside analogue inhibitors [11].

Non-structural protein 15 (NendoU) is a uridylate-specific endoribonuclease [20]. The catalytic activity of MERS-CoV nsp15 can be modulated by interactions with other nsps (e.g. nsp8 and a nsp7/8 complex), oligomeric assembly and RNA binding efficiency. Nsp15 is essential in coronavirus biology, but interestingly its deletion does not disrupt replication, so its principal action remains elusive. A resolved X-ray structure has been published and deposited with the RCSB Protein Data Bank (6W01) [9]. This shows that enzymatic functional arises from a hexameric complex whose similarity to SARS-CoV nsp15 suggests that inhibitors of this older coronavirus may also inhibit the more recently identified one. MERS-CoV nsp15 inhibitors are considered to be unlikely to inhibit SARS-CoV-2 nsp15.

Non-structural protein 16 dimerises with nsp10 to form a 2'-O-methyltransferase that mediates 2'-O-ribose methylation to the 5'-cap structure of viral mRNAs [3], and this activity helps to improve viral protein translation, to limit host immune detection and inhibit the host's anti-viral interferon response [14]. High-resolution structures of the SARS-CoV-2 nsp16/10 heterodimer have been reported (see for example PDB ID 6W4H) [13]. Such analysis reveals any domains that could be exploited for the development of antiviral inhibitors, which could act to either prevent substrate interaction or block heterodimer formation.

References

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1. Adedeji AO, Marchand B, Te Velthuis AJ, Snijder EJ, Weiss S, Eoff RL, Singh K, Sarafianos SG. (2012) Mechanism of nucleic acid unwinding by SARS-CoV helicase. PLoS ONE, 7 (5): e36521. [PMID:22615777]

2. Ahn DG, Choi JK, Taylor DR, Oh JW. (2012) Biochemical characterization of a recombinant SARS coronavirus nsp12 RNA-dependent RNA polymerase capable of copying viral RNA templates. Arch Virol, 157 (11): 2095-104. [PMID:22791111]

3. Bouvet M, Debarnot C, Imbert I, Selisko B, Snijder EJ, Canard B, Decroly E. (2010) In vitro reconstitution of SARS-coronavirus mRNA cap methylation. PLoS Pathog, 6 (4): e1000863. [PMID:20421945]

4. Bouvet M, Imbert I, Subissi L, Gluais L, Canard B, Decroly E. (2012) RNA 3'-end mismatch excision by the severe acute respiratory syndrome coronavirus nonstructural protein nsp10/nsp14 exoribonuclease complex. Proc Natl Acad Sci USA, 109 (24): 9372-7. [PMID:22635272]

5. Dong S, Sun J, Mao Z, Wang L, Lu YL, Li J. (2020) A guideline for homology modeling of the proteins from newly discovered betacoronavirus, 2019 novel coronavirus (2019-nCoV). J Med Virol, 92 (9): 1542-1548. [PMID:32181901]

6. Fung TS, Liu DX. (2019) Human Coronavirus: Host-Pathogen Interaction. Annu Rev Microbiol, 73: 529-557. [PMID:31226023]

7. Gordon CJ, Tchesnokov EP, Woolner E, Perry JK, Feng JY, Porter DP, Götte M. (2020) Remdesivir is a direct-acting antiviral that inhibits RNA-dependent RNA polymerase from severe acute respiratory syndrome coronavirus 2 with high potency. J Biol Chem, 295 (20): 6785-6797. [PMID:32284326]

8. Imbert I, Guillemot JC, Bourhis JM, Bussetta C, Coutard B, Egloff MP, Ferron F, Gorbalenya AE, Canard B. (2006) A second, non-canonical RNA-dependent RNA polymerase in SARS coronavirus. EMBO J, 25 (20): 4933-42. [PMID:17024178]

9. Kim Y, Jedrzejczak R, Maltseva NI, Wilamowski M, Endres M, Godzik A, Michalska K, Joachimiak A. (2020) Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2. Protein Sci, 29 (7): 1596-1605. [PMID:32304108]

10. Peng Q, Peng R, Yuan B, Zhao J, Wang M, Wang X, Sun Y, Fan Z, Qi J, Gao GF et al.. (2020) Structural and biochemical characterization of nsp12-nsp7-nsp8 core polymerase complex from SARS-CoV-2. Cell Reports,. DOI: 10.1016/j.celrep.2020.107774

11. Pruijssers AJ, Denison MR. (2019) Nucleoside analogues for the treatment of coronavirus infections. Curr Opin Virol, 35: 57-62. [PMID:31125806]

12. Ramsey JR, Shelton PMM, Heiss TK, Olinares PDB, Vostal LE, Soileau H, Warrington S, Adaniya S, Miller M, Sun S et al.. (2023) Using a function-first 'scout fragment'-based approach to develop allosteric covalent inhibitors of conformationally dynamic helicase mechanoenzymes. bioRxiv, Preprint. DOI: 10.1101/2023.09.25.559391 [PMID:37808863]

13. Rosas-Lemus M, Minasov G, Shuvalova L, Inniss NL, Kiryukhina O, Brunzelle J, Satchell KJF. (2020) High-resolution structures of the SARS-CoV-2 2′-O-methyltransferase reveal strategies for structure-based inhibitor design. Science Signaling, 13 (651): eabe1202. DOI: 10.1126/scisignal.abe1202

14. Schindewolf C, Lokugamage K, Vu M, Johnson BA, Scharton D, Plante JA, Kalveram BK, Crocquet-Valdes PA, Sotcheff SL, Jaworski E et al.. (2022) SARS-CoV-2 Uses Nonstructural Protein 16 to Evade Restriction by IFIT1 and IFIT3. bioRxiv, Preprint. DOI: 10.1101/2022.09.26.509529

15. Tanner JA, Watt RM, Chai YB, Lu LY, Lin MC, Peiris JS, Poon LL, Kung HF, Huang JD. (2003) The severe acute respiratory syndrome (SARS) coronavirus NTPase/helicase belongs to a distinct class of 5' to 3' viral helicases. J Biol Chem, 278 (41): 39578-82. [PMID:12917423]

16. Wang W, Zhou Z, Xiao X, Tian Z, Dong X, Wang C, Li L, Ren L, Lei X, Xiang Z et al.. (2021) SARS-CoV-2 nsp12 attenuates type I interferon production by inhibiting IRF3 nuclear translocation. Cell Mol Immunol, 18 (4): 945-953. [PMID:33637958]

17. Wang Y, Anirudhan V, Du R, Cui Q, Rong L. (2021) RNA-dependent RNA polymerase of SARS-CoV-2 as a therapeutic target. J Med Virol, 93 (1): 300-310. [PMID:32633831]

18. 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 volume, 39: 198–216. DOI: 10.1007/s10930-020-09901-4

19. Zaher NH, Mostafa MI, Altaher AY. (2020) Design, synthesis and molecular docking of novel triazole derivatives as potential CoV helicase inhibitors. Acta Pharm, 70 (2): 145-159. [PMID:31955138]

20. Zhang L, Li L, Yan L, Ming Z, Jia Z, Lou Z, Rao Z. (2018) Structural and Biochemical Characterization of Endoribonuclease Nsp15 Encoded by Middle East Respiratory Syndrome Coronavirus. J Virol, 92 (22). [PMID:30135128]

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