Targeting SARS-CoV-2 Proteases for COVID-19 Antiviral Development

Abstract

The emergence of severe acute respiratory syndrome (SARS-CoV-2) in 2019 marked the third occurrence of a highly pathogenic coronavirus in the human population since 2003. As the death toll surpasses 5 million globally and economic losses continue, designing drugs that could curtail infection and disease progression is critical. In the US, three highly effective Food and Drug Administration (FDA)–authorized vaccines are currently available, and Remdesivir is approved for the treatment of hospitalized patients. However, moderate vaccination rates and the sustained evolution of new viral variants necessitate the ongoing search for new antivirals. Several viral proteins have been prioritized as SARS-CoV-2 antiviral drug targets, among them the papain-like protease (PLpro) and the main protease (Mpro). Inhibition of these proteases would target viral replication, viral maturation, and suppression of host innate immune responses. Knowledge of inhibitors and assays for viruses were quickly adopted for SARS-CoV-2 protease research. Potential candidates have been identified to show inhibitory effects against PLpro and Mpro, both in biochemical assays and viral replication in cells. These results encourage further optimizations to improve prophylactic and therapeutic efficacy. In this review, we examine the latest developments of potential small-molecule inhibitors and peptide inhibitors for PLpro and Mpro, and how structural biology greatly facilitates this process.

Gain-of-Signal Assays for Probing Inhibition of SARS-CoV-2 M pro /3CL pro in Living Cells

“…Multiple small-molecule inhibitors of M pro have been described, including GC376 and boceprevir, with in vitro 50% inhibitory concentration (IC 50 ) values of 0.03 to 0.19 μM and 1.6 to 8.0 μM, respectively ( 8 , 27 , 28 ). GC376 was developed against a panel of 3C and 3C-like cysteine proteases ( 29 , 30 ), and boceprevir was developed as an inhibitor of the NS3 protease of hepatitis C virus ( 1 , 31 , 32 ).…”

“…SARS-CoV-2 (SARS2) has two proteases, papain-like protease (PL pro , Nsp3) and main protease/3C-like protease (M pro , 3CL pro , Nsp5), which are responsible for 3 (Nsp1-4) and 11 (Nsp4-16) viral polyprotein cleavage events, respectively ( 4 – 7 ). These cleavage events are essential for the formation of the viral replicase complex and pathogenesis, and therefore, both of these SARS2 proteases are under intensive investigation for the development of drugs to combat the ongoing COVID-19 pandemic ( 8 ).…”

The effect of various compounds on the COVID mechanisms, from chemical to molecular aspects

“…In fact, gamma-lactam rings, for example, are frequently substituted for carbonyl groups. Besides, some studies, have attempted to design drugs by adding non-polar and aromatic groups to the compounds in order to reduce the amount of drug-protein binding in the blood and the volume of distribution in the body while also increasing the drug's tropism within the lungs [ 153 ]. It is worth noting that virtual screening of potential Mpro inhibitors has also confirmed that Lewis acid structures such as bortezomib, which contains boron metal bind to M-protein with ease [ 154 ].…”

A strategy for evaluating antiviral resistance: Application to small molecule drugs/inhibitors against SARS-CoV-2

“…Monomeric M pro consists of an N-terminal finger (residues 1-7) and three domains: the chymotrypsin-like domain I (residues 8-101), the picornavirus 3C protease-like domain II (residues 102-184) and domain III (residues 201-306) 42 . Dimerization is needed for M pro function, as interaction between the protomers, in particular the interaction between the Nterminal S1 of one protomer and E166 of the other promoter, keeps the enzyme in an active conformation 37 .…”

“…However, due to its low oral bioavailability, it has been superseded by the oral drug, PF-07321332 (EUA-approved nirmatrelvir), which does not interact with any residue under positive selection pressure. Interestingly, G15, K90, and P132, which are often mutated in current SARS-CoV-2 variants of concern 42 , are under positive selection. Since the mutation of K90 to Arg is expected to improve dimerization 42 , it may affect compounds that target the dimer interface.…”