Recent Advances on Targeting Proteases for Antiviral Development

Abstract

Viral proteases are an important target for drug development, since they can modulate vital pathways in viral replication, maturation, assembly and cell entry. With the (re)appearance of several new viruses responsible for causing diseases in humans, like the West Nile virus (WNV) and the recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), understanding the mechanisms behind blocking viral protease's function is pivotal for the development of new antiviral drugs and therapeutical strategies. Apart from directly inhibiting the target protease, usually by targeting its active site, several new pathways have been explored to impair its activity, such as inducing protein aggregation, targeting allosteric sites or by inducing protein degradation by cellular proteasomes, which can be extremely valuable when considering the emerging drug-resistant strains. In this review, we aim to discuss the recent advances on a broad range of viral proteases inhibitors, therapies and molecular approaches for protein inactivation or degradation, giving an insight on different possible strategies against this important class of antiviral target.

Keywords: PROTACs; antiviral therapies; covalent inhibitors; natural products; peptidomimetics; viral proteases.

Figure 1

Past pandemics and current outbreaks throughout the world [1,2]. Created with BioRender.com.

Figure 2

Simplified viral entry and replication mechanism. Created with BioRender.com.

Figure 3

Schechter–Berger nomenclature for substrate recognition by proteases. Created with BioRender.com.

Figure 4

Protease cleavage mechanisms. Created with BioRender.com.

Figure 5

Nirmatrelvir bound to SARS-CoV-2 M^pro (PDB ID: 7TE0). The nitrile warhead is depicted in purple. Created with BioRender.com.

Figure 6

Compounds designed by Phoo et al. [48]. Created with BioRender.com.

Figure 7

Macrocyclic HCV NS3/4A protease inhibitors and derivatives. R groups depicted in blue are shown in the box on the right. Created with BioRender.com.

Figure 8

Examples of electrophilic warheads used for targeting proteases. Created with BioRender.com.

Figure 9

General structure of SMAIs developed by Li et al. [58] (A) Masked aldehyde warheads’ (in blue) mechanism of inhibition. (B) Bioisosteric replacement of γ-lactam ring via 2-pyridone moiety and anti-SARS-CoV-2 activity. Created with BioRender.com.

Figure 10

In silico-discovered protease inhibitors. Created with BioRender.com.

Figure 11

Allosteric inhibition mechanisms by small molecule. Created with BioRender.com.

Figure 12

Interaction of aryl triazole derivative (compound 28, in orange) at the dimer interface of the protease (PDB ID: 7TCZ). Each chain is represented in different colors (blue and light red), and the catalytic triad (His63-His157-Ser163) is represented in dark red. Created with BioRender.com.

Figure 13

Viral entry mechanisms for SARS-CoV-2 and influenza and the role of a host’s proteases. Created with BioRender.com.

Figure 14

Molecular mechanism of protein ubiquitination and protein degradation by proteasome. Created with BioRender.com.

Figure 15

All five proteasome inhibitors were able to inhibit ZIKV and DENV viral replication.

Figure 16

PROTAC mechanism of action. Created with BioRender.com.

Figure 17

INM-based PROTACs developed by Desantis et al. [148] with broad spectrum activity against coronaviruses. Created with BioRender.com.

Figure 18

Thalidomide-based PROTACs developed by Alugubelli et al. [149] and Hahn et al. [151] with diverse antiviral activities. Created with BioRender.com.

Figure 19

Bioactive compounds with protease activity. Created with BioRender.com.