Antiviral evaluation of hydroxyethylamine analogs: Inhibitors of SARS-CoV-2 main protease (3CLpro), a virtual screening and simulation approach

Abstract

The continued toll of COVID-19 has halted the smooth functioning of civilization on a global scale. With a limited understanding of all the essential components of viral machinery and the lack of structural information of this new virus, initial drug discovery efforts had limited success. The availability of high-resolution crystal structures of functionally essential SARS-CoV-2 proteins, including 3CLpro, supports the development of target-specific therapeutics. 3CLpro, the main protease responsible for the processing of viral polypeptide, plays a vital role in SARS-CoV-2 viral replication and translation and is an important target in other coronaviruses. Additionally, 3CLpro is the target of repurposed drugs, such as lopinavir and ritonavir. In this study, target proteins were retrieved from the protein data bank (PDB IDs: 6M03, 6LU7, 2GZ7, 6W63, 6SQS, 6YB7, and 6YVF) representing different open states of the main protease to accommodate macromolecular substrate. A hydroxyethylamine (HEA) library was constructed from harvested chemical structures from all the series being used in our laboratories for screening against malaria and Leishmania parasites. The database consisted of ∼1000 structure entries, of which 70% were new to ChemSpider at the time of screening. This in-house library was subjected to high throughput virtual screening (HTVS), followed by standard precision (SP) and then extra precision (XP) docking (Schrodinger LLC 2021). The ligand strain and complex energy of top hits were calculated by Molecular Mechanics Generalized Born Surface Area (MM/GBSA) method. Promising hit compounds (n=40) specifically binding to 3CLpro with high energy and average MM/GBSA scores were then subjected to (100-ns) MD simulations. Using this sequential selection followed by an in-silico validation approach, we found a promising HEA-based compound (N,N'-((3S,3'S)-piperazine-1,4-diylbis(3-hydroxy-1-phenylbutane-4,2-diyl))bis(2-(5-methyl-1,3-dioxoisoindolin-2-yl)-3-phenylpropanamide)), which showed high in vitro antiviral activity against SARS-CoV-2. Further to reduce the size of the otherwise larger ligand, a pharmacophore-based predicted library of ∼42 derivatives was constructed, which were added to the previous compound library and rescreened virtually. Out of several hits from the predicted library, two compounds were synthesized, tested against SARS-CoV-2 culture, and found to have markedly improved antiviral activity.

A potent candidate against Zika virus infection: Synthesis, bioactivity, radiolabeling and biodistribution studies

“…19 Recently, several HEA analogs have been reported as efficacious against the SARS-CoV-2 virus. 20–22 FDA-approved protease inhibitors of HIV 18 also support the importance of the HEA pharmacophore (Fig. 1).…”

Recent updates on the biological efficacy of approved drugs and potent synthetic compounds against SARS-CoV-2

“…The compound ( XXV ) was synthesized by the authors and has been evaluated for biological efficacy against the virus in cell media and depicted excellent results with an IC 50 value of 4.973 μM. In another report, Gupta et al 67 followed a similar methodology and suggested the strong binding affinity of three HEA-based compounds against the main protease of SARS-CoV-2. The best result among these was displayed by compound XXVI , an IC 50 value of 6.38 μM.…”

In Silico Binding of 2-Aminocyclobutanones to SARS-CoV-2 Nsp13 Helicase and Demonstration of Antiviral Activity

“…A continued effort is warranted to explore new key targets for effective drug development against SARS-CoV-2 and new variants [ 10 ]. Target-based drug development is the most rapid pipeline to deliver potent molecules even from weaker initial hits [ 11 ].…”