Identify potent SARS-CoV-2 main protease inhibitors via accelerated free energy perturbation-based virtual screening of existing drugs

Abstract

The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global crisis. There is no therapeutic treatment specific for COVID-19. It is highly desirable to identify potential antiviral agents against SARS-CoV-2 from existing drugs available for other diseases and thus repurpose them for treatment of COVID-19. In general, a drug repurposing effort for treatment of a new disease, such as COVID-19, usually starts from a virtual screening of existing drugs, followed by experimental validation, but the actual hit rate is generally rather low with traditional computational methods. Here we report a virtual screening approach with accelerated free energy perturbation-based absolute binding free energy (FEP-ABFE) predictions and its use in identifying drugs targeting SARS-CoV-2 main protease (Mpro). The accurate FEP-ABFE predictions were based on the use of a restraint energy distribution (RED) function, making the practical FEP-ABFE−based virtual screening of the existing drug library possible. As a result, out of 25 drugs predicted, 15 were confirmed as potent inhibitors of SARS-CoV-2 Mpro. The most potent one is dipyridamole (inhibitory constant Ki = 0.04 µM) which has shown promising therapeutic effects in subsequently conducted clinical studies for treatment of patients with COVID-19. Additionally, hydroxychloroquine (Ki = 0.36 µM) and chloroquine (Ki = 0.56 µM) were also found to potently inhibit SARS-CoV-2 Mpro. We anticipate that the FEP-ABFE prediction-based virtual screening approach will be useful in many other drug repurposing or discovery efforts.

Targeting the Main Protease of SARS‐CoV‐2: From the Establishment of High Throughput Screening to the Design of Tailored Inhibitors

“…[3,[10][11][12][13] It has been reported that as horter,i nternally quenched fluorescent peptide substrate MCA-Ala-Val-Leu-Gln-Ser-Gly-Phe-Arg-Lys(Dnp)-Lys-NH 2 equipped with 7methoxy-coumarin-4-yl-acetic acid (MCA)a sf luorophore and the 2,4-dinitrophenyl (Dnp) quencher can also be used to monitor SARS-CoV-2 M pro . [4,14,15] Both internally quenched substrates share aP 4-to-P4' consensus sequence.…”

Identification of Potential SARS-CoV-2 Main Protease and Spike Protein Inhibitors from the Genus Aloe: An In Silico Study for Drug Development

“…Chloroquine and its analogues are diprotic weak bases that in their unprotonated forms, readily diffuse through cellular and organelle membranes such as lysosomes, endosomes and Golgi vesicles increasing pH from 6.3 to 6.7 [32][33][34]. In addition to disruption of endocytic pathway pH, chloroquine and hydroxychloroquine have been recently found to be potent inhibitors of SARS-CoV-2 M pro but not viruses that belong to Rhabdoviridae [35]. In our study, the compounds previously isolated from Aloe plants were virtually screened against SARS-CoV-2 main protease M pro (PDB ID: 6LU7) ( Figure 2) and spike glycoprotein (PDB ID: 6M0J) ( Figure 2) to find potential inhibitors for SARS-CoV-2.…”

Die Hauptprotease von SARS‐CoV‐2 als Zielstruktur: Von der Etablierung eines Hochdurchsatz‐Screenings zum Design maßgeschneiderter Inhibitoren

“…Die beobachtete Zeit-abhängige Inhibition wies darauf hin, dass diese Indolester ihren Effekt durch Acylierung des Cysteins im aktiven Zentrum vermitteln (siehe auch Abbildung S16), in Übereinstimmung mit Literaturdaten. [25,26] Während die Mehrheit der Indolester (11)(12)(13)(14)(15)(16)(17)(18)(19)a ls pseudo-irreversible Inhibitoren charakterisiert werden konnte,z eigten einige der Verbindungen (Tabelle S1) eine Enzym-Reaktivierung innerhalb einer Messzeit von einer Abbildung 4. Vorgeschlagene Bindungspose des Azapeptidnitrils 8 (orange) im aktiven Zentrum der SARS-CoV-2-M pro mit den relevanten Aminosäuren (grün).…”

“…[3,[10][11][12][13] Des Weiteren wurde auch ein kürzeres intern gequenchtes,fluoreszierendes Peptidsubstrat, MCA-Ala-Val-Leu-Gln-Ser-Gly-Phe-Arg-Lys(Dnp)-Lys-NH 2 mit 7-Methoxycumarin-4-yl-essigsäure (MCA)a ls Fluorophor und einem 2,4-Dinitrophenyl(Dnp)-Quencher,e ingesetzt, um die SARS-CoV-2-M pro -Reaktion zu verfolgen. [4,14,15] Beide intern gequenchten Substrate besitzen eine P4-P4'-Konsensus-Sequenz.…”

“…= O, Tabelle 3) in 20 führte zu einem Inhibitor mit hoher Affinität( IC 50 = 5.41 nm), aber ausgeprägter M pro -Reaktivierung.W ir analysierten die Struktur-Wirkungs-Beziehungen der irreversibel bindenden Indolester mit derselben 5-Chlorpyridin-3-olat-Abgangsgruppe (X = NH, Y = Cl;[11][12][13][14][15][16][17]19).…”