Main and papain-like proteases as prospective targets for pharmacological treatment of coronavirus SARS-CoV-2

Abstract

The pandemic caused by the coronavirus SARS-CoV-2 led to a global crisis in the world healthcare system. Despite some progress in the creation of antiviral vaccines and mass vaccination of the population, the number of patients continues to grow because of the spread of new SARS-CoV-2 mutations. There is an urgent need for direct-acting drugs capable of suppressing or stopping the main mechanisms of reproduction of the coronavirus SARS-CoV-2. Several studies have shown that the successful replication of the virus in the cell requires proteolytic cleavage of the protein structures of the virus. Two proteases are crucial in replicating SARS-CoV-2 and other coronaviruses: the main protease (Mpro) and the papain-like protease (PLpro). In this review, we summarize the essential viral proteins of SARS-CoV-2 required for its viral life cycle as targets for chemotherapy of coronavirus infection and provide a critical summary of the development of drugs against COVID-19 from the drug repurposing strategy up to the molecular design of novel covalent and non-covalent agents capable of inhibiting virus replication. We overview the main antiviral strategy and the choice of SARS-CoV-2 Mpro and PLpro proteases as promising targets for pharmacological impact on the coronavirus life cycle.

Fig. 1. SARS-CoV-2 genome encoding 5 structural proteins and 16 non-structural proteins (Nsp) translated into a single polyprotein chain (PP1ab). Red (PLpro) and blue (Mpro) triangles show the cleavage sites of the polyprotein chain by proteases. Reproduced with permission from ref. . © 2021 Elsevier B.V. All rights reserved.

Fig. 2. (a) The S protein of SARS-CoV-2 (Omicron S-open-2, PDB: 7WVO): chains A–C with receptor-binding domain (RBD). (b) Cryo-EM structure of SARS-CoV-2 spike protein in complex with angiotensin-converting enzyme 2 (ACE2) shown in gold (PDB: 8HFZ). A close-up representation of the RBD protein and ACE2 interface. The sticks represent the key residues that interact with the ACE2. Numerous atomic connections are made between SARS-CoV-2 RBD (violet) and ACE2 (gold).

Fig. 3. (a) Crystal structure of the N-terminal RNA-binding domain of the nucleocapsid protein (PDB: 6M3M) and (b) the C-terminal dimerization domain of the SARS-CoV-2 nucleocapsid (PDB: 6ZCO).

Fig. 4. Structure of the SARS-CoV-2 E-protein pentameric ion channel (PDB: 5X29): (a) top and (b) side views. (c) The pentameric structure of the transmembrane domain of the E-protein of SARS-CoV-2: (PDB: 7K3G).

Fig. 5. (a) Crystal structure of the membrane protein (M-protein) of the coronavirus SARS-COV-2 (PDB: 8CTK). (b) Structural components of the M protein: two transmembrane three-helical bundles (TM1, TM2, TM3) and two intravirion Hinge domains and C-terminal β-sheet sandwich domain (BD).

Fig. 6. (a) Cryo-electron microscope structure of the nsp12–nsp7–nsp8 complex (PDB: 7BV1). (b) The nsp12–nsp7–nsp8 complex associated with the template primer RNA and remdesivir triphosphate (RTP) (PDB: 7BV2).

Fig. 7. Some nucleoside analogs available for the treatment of COVID-19.

Fig. 8. Mechanism of action of cysteine proteases. Reproduced with permission from ref. . © 2020 Elsevier Ltd. All rights reserved.

Fig. 9. Crystal structure of SARS-CoV-2 main protease (Mpro) with the catalytic center (His41 and Cys145) (PDB: 6LU7): domain I – cyan, domain II – violet, domain III – blue.

Fig. 10. Structure of Perampanel analogs inhibiting the activity of Mpro.

Fig. 11. Structure of noncovalent Mpro inhibitors based on ML300 scaffold.

Fig. 12. Structure of non-covalent inhibitor MCULE-5948770040 and its optimized hits.

Fig. 13. A noncovalent orally active agent Ensitrelvir (S-217622) and its analogs with strong broad-spectrum anticoronaviral activities.

Fig. 14. (A) Structure of noncovalent inhibitors of SARS-CoV-2 Mpro, containing an isoquinoline ring and a bromophenyl ring. (B) The binding of noncovalent inhibitor WU-04 into the catalytic pocket of SARS-CoV-2 Mpro. (C) Seven hit analogs of WU-04 and their inhibitory activity against SARS-CoV-2 Mpro evaluated using the fluorescent assay. Adapted with permission from ref. . Copyright © 2023 The Authors. Published by American Chemical Society.

Fig. 15. Direct-acting covalent inhibitors of Mpro that exploited the gem-dimethyl effect.

Fig. 16. Different mechanisms of covalent Mpro inhibition, involving α-ketoamides, aldehydes, and nitriles. Reproduced with permission from ref. . © 2023 by the authors. Licensee MDPI, Basel, Switzerland.

Fig. 17. Reported peptidomimetic Mpro inhibitors with the high inhibitory activities (μM).

Fig. 18. Chemical structure of Narlaprevir, Boceprevir and Nirmatrelvir.

Fig. 19. PLpro structure: terminal ubiquitin-like (Ubl) domain, zinc-binding domain, and catalytic thumb-palm domain. The catalytic active site containing the catalytic triad Cys111-His272-Asp286 (shaded circle) (PDB: 6WX4).

Fig. 20. X-ray structure of PLpro in complex with covalent peptide inhibitor VIR250 (PDB: 6WUU).

Fig. 21. Highly potent inhibitors of PLpro designed on a scaffold of the naphthalene-based inhibitor GRL-0617.

Fig. 22. Structurally diverse inhibitors of PLpro enzyme of SARS-CoV-2.

Fig. 23. Dual-targeting inhibitors against Mpro and PLpro enzymes.

Fig. 24. Forodesine and Riboprine as dual acting inhibitors against RdRp and ExoN enzymes of SARS-CoV-2.