A Review of the Current Landscape of SARS-CoV-2 Main Protease Inhibitors: Have We Hit the Bullseye Yet?

Abstract

In this review, we collected 1765 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) M-pro inhibitors from the bibliography and other sources, such as the COVID Moonshot project and the ChEMBL database. This set of inhibitors includes only those compounds whose inhibitory capacity, mainly expressed as the half-maximal inhibitory concentration (IC₅₀) value, against M-pro from SARS-CoV-2 has been determined. Several covalent warheads are used to treat covalent and non-covalent inhibitors separately. Chemical space, the variation of the IC₅₀ inhibitory activity when measured by different methods or laboratories, and the influence of 1,4-dithiothreitol (DTT) are discussed. When available, we have collected the values of inhibition of viral replication measured with a cellular antiviral assay and expressed as half maximal effective concentration (EC₅₀) values, and their possible relationship to inhibitory potency against M-pro is analyzed. Finally, the most potent covalent and non-covalent inhibitors that simultaneously inhibit the SARS-CoV-2 M-pro and the virus replication in vitro are discussed.

Keywords: 3CL-pro inhibitors; COVID-19; M-pro inhibitors; computational chemistry; protease inhibitors; virtual screening.

Figure 1

SARS-CoV-2 M-pro structure. (A) Biological assembly of the M-pro in its dimeric form. The left protomer is shown in cartoon representation, colored by protein secondary structure, and the right protomer is displayed as a surface. (B) Detailed snapshot of the catalytic water, Cys145 and His41.

Figure 2

Violin plots of the pIC₅₀ values from 552 putative covalent and 1213 non-covalent SARS-CoV-2 M-pro inhibitors.

Figure 3

t-Distributed Stochastic Neighbor Embedding (t-SNE) visualization of the chemical space of a set of SARS-CoV-2 M-pro inhibitors extracted from the bibliography. Embedding is based on the 2048-bit Morgan fingerprint. Markers are colored according to several manually attributed chemotypes.

Figure 4

Comparison of multiple pIC₅₀ values calculated by different laboratories. The pIC₅₀ values of the five most evaluated compounds, GC376, boceprevir, ebselen, disulfiram and telaprevir, are shown as white points to highlight that different laboratories and methods can estimate different pIC₅₀ values.

Figure 5

Effect of 1mM of DTT on M-pro inhibition in a group of 246 SARS-CoV-2 M-pro inhibitors [77]. A gray line represents the points where the presence of DTT does not affect the % of inhibition. Compounds far below the gray line are DTT-sensitive inhibitors and are colored orange. Compounds near the gray line are DTT insensitive inhibitors and are colored blue. The R² value of the insensitive compounds is 0.75 (p = 1.1 × 10⁻²⁷).

Figure 6

Comparison between the pIC₅₀ values of some SARS-CoV-2 M-pro inhibitors and their antiviral activities, measured as pEC₅₀ values. To avoid comparisons between values from different laboratories, data from five articles that calculate the pIC₅₀ and pEC₅₀ for a set of compounds are shown independently. The PubMedID of the articles is indicated. A gray line represents the diagonal where pIC₅₀ and pEC₅₀ values are equal.

Figure 7

The 15 most potent non-covalent inhibitors of the SARS-CoV-2 M-pro. Only M-pro inhibitors with pIC₅₀ values that can inhibit SARS-CoV-2 replication in a cellular antiviral assay are shown. pIC₅₀ values are shown in parentheses.

Figure 8

The 15 most potent covalent inhibitors of the SARS-CoV-2 M-pro. Only M-pro inhibitors with pIC₅₀ values that can inhibit the SARS-CoV-2 replication in a cellular antiviral assay are shown. pIC₅₀ values are shown in parentheses.