Structure-Guided Design of Potent Inhibitors of SARS-CoV-2 3CL Protease: Structural, Biochemical, and Cell-Based Studies.

Abstract

<p>We describe herein the results of our studies related to the application of X-ray crystallography, the Thorpe-Ingold effect, deuteration, and stereochemistry in the design of highly potent and non-toxic inhibitors of SARS-CoV-2 3CLpro to combat SARS-CoV-2 and emerging variants.</p>

The SARS‐CoV‐2 main protease (Mpro): Structure, function, and emerging therapies for COVID‐19

“…The ongoing COVID‐19 pandemic has created a serious threat to human health and life safety worldwide, thus, there is an urgent medical need to find more effective therapeutic strategies for combating COVID‐19 300–303 . Among all validated targets for fighting CoVs, including SARS‐CoV‐2, the highly conserved 3D structure of 3CL pro plays an essential role in CoV replication, and no known human protease possesses a similar cleavage specificity, making 3CL pro an ideal target for developing clinically effective anti‐SARS‐CoV‐2 agents 21,60,109,304,305 . It is worth noting that a wide range of compounds have been found to have strong to moderate SARS‐CoV‐2 3CL pro inhibitory effects in the past few years.…”

“…[300][301][302][303] Among all validated targets for fighting CoVs, including SARS-CoV-2, the highly conserved 3D structure of 3CL pro plays an essential role in CoV replication, and no known human protease possesses a similar cleavage specificity, making 3CL pro an ideal target for developing clinically effective anti-SARS-CoV-2 agents. 21,60,109,304,305 It is worth noting that a wide range of compounds have been found to have strong to moderate SARS-CoV-2 3CL pro inhibitory effects in the past few years. To better understand the structural features of SARS-CoV-2 3CL pro inhibitors and their inhibitory mechanisms, this study systematically summarized the reported structurally diverse SARS-CoV-2 3CL pro inhibitors (including marketed drugs and other synthetic compounds, herbal constituents, and their derivatives), as well as their inhibition potentials and mechanisms of action.…”

“…107,108 Moreover, by using the fluorine-walk approach to explore the binding modes of the F-substituted phenyl ring, they found that compounds 15b and 15c were the most effective against SARS-CoV-2 3CL pro , with IC 50 values of 0.13 and 0.17 μM, respectively. 109 Compounds 6j and 6h inhibited SARS-CoV-2 3CL pro with significant efficacy, while administration of compound 6j significantly improved survival, reductions in lung virus titers, and lung histopathology throughout the day in a mouse model of MERS-CoV infection. 80 Several non-deuterated and deuterated compounds containing a conformationally constrained cyclohexane moiety were synthesized, of which compound 2a/3a displayed high potency in biochemical assays with IC 50 values in the submicromolar range.…”

“…As a result of the multiple advantages of introducing deuterium into the drug, the deuterated variants at the R‐site exhibited a significant increase in the anti‐3CL pro and cell‐based assays, as well as improved pharmacokinetics and reduced toxicity 107,108 . Moreover, by using the fluorine‐walk approach to explore the binding modes of the F‐substituted phenyl ring, they found that compounds 15b and 15c were the most effective against SARS‐CoV‐2 3CL pro , with IC 50 values of 0.13 and 0.17 μM, respectively 109 . Compounds 6j and 6h inhibited SARS‐CoV‐2 3CL pro with significant efficacy, while administration of compound 6j significantly improved survival, reductions in lung virus titers, and lung histopathology throughout the day in a mouse model of MERS‐CoV infection 80 .…”

Structure-Guided Design of Potent Spirocyclic Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3C-like Protease

“…45 Biochemical Studies. The inhibitory activity of compounds 1−18b/c toward SARS-CoV-2 3CL pro and MERS-CoV 3CLpro in biochemical assays [23][24][25]28 as well as the cytotoxicity of the compounds were determined, and the results are listed in Tables 1 and 2. For comparative purposes, the IC 50 and CC 50 values of GC376 are included in Table 1.…”