Identification of a novel inhibitor of SARS‐CoV‐2 main protease: an in silico, biochemical, and cell‐based approach

• Published in: The FEBS journal Vol. 290; no. 23; pp. 5496 - 5513
• Main Authors: Trivedi, Aditya, Kardam, Vandana, Inampudi, Krishna Kishore, Vrati, Sudhanshu, Gupta, Dharmender, Singh, Aekagra, Kayampeta, Sarala Rani, Appaiahgari, Mohan Babu, Sehgal, Deepak
• Format: Journal Article
• Language: English
• Published: England Blackwell Publishing Ltd 01.12.2023
• Subjects: Antiviral activity; Antiviral Agents - chemistry; Antiviral Agents - pharmacology; Cell culture; coronavirus; Coronaviruses; COVID-19; HCoV‐229E; Humans; in silico; Inhibitors; Molecular Docking Simulation; Mpro; Natural products; Pandemics; Protease; Protease Inhibitors - chemistry; Protease Inhibitors - pharmacology; SARS-CoV-2; Severe acute respiratory syndrome; Severe acute respiratory syndrome coronavirus 2; STL522228; Therapeutic applications; Vaccines; Viral diseases; coronavirus; SARS-CoV-2; HCoV-229E; in silico; STL522228; Mpro
• ISSN: 1742-464X; 1742-4658
• DOI: 10.1111/febs.16947

The recurrent nature of coronavirus outbreaks, severity of the COVID‐19 pandemic, rapid emergence of novel variants, and concerns over the effectiveness of existing vaccines against novel variants have highlighted the need to develop therapeutic interventions. Targeted efforts to identify inhibitors of crucial viral proteins are the preferred strategy. In this study, we screened FDA‐approved and natural product libraries using in silico approach for potential hits against the SARS‐CoV‐2 main protease (Mpro) and experimentally validated their potency using in vitro biochemical and cell‐based assays. Seven potential hits were identified through in silico screening and were subsequently evaluated in SARS‐CoV‐2‐based cell‐free assays, followed by testing in the HCoV‐229E‐based culture system. Of the tested compounds, 4‐(3,4‐dihydroxyphenyl)‐6,7‐dihydroxy‐1‐isopropyl‐1H‐benzofuro[3,2‐b]pyrazolo[4,3‐e]pyridin‐3(2H)‐one (PubChem CID:71755304, hereafter referred to as STL522228) exhibited significant antiviral activity. Subsequently, its potential as a novel COVID therapeutic molecule was validated in the SARS‐CoV‐2‐culture system, where STL522228 demonstrated superior antiviral activity (EC50 = 0.44 μm) compared to Remdesivir (EC50 = 0.62 μm). Based on these findings, we report the strong anti‐coronavirus activity of STL522228, and propose that it as a promising pan‐coronavirus Mpro inhibitor for further experimental and preclinical validation. The recurrent nature of coronavirus outbreaks, severity of the COVID‐19 pandemic, rapid emergence of novel variants, and concerns over the effectiveness of existing vaccines against novel variants have highlighted the need to develop appropriate therapeutic interventions. Here, Deepak Sehgal and colleagues utilised an in silico, biochemical and cell‐based strategy, and identified STL522228, which demonstrates considerable antiviral efficacy in an HCoV‐229E system and better activity in the SARS CoV‐2 system compared to Remdesivir. STL522228 shows promise for further development as a coronavirus Mpro inhibitor.