Discovery of Natural Bisbenzylisoquinoline Analogs from the Library of Thai Traditional Plants as SARS-CoV-2 3CL Pro Inhibitors: In Silico Molecular Docking, Molecular Dynamics, and In Vitro Enzymatic Activity

• Published in: Journal of chemical information and modeling 2023-04, Vol.63 (7), p.2104-2121
• Main Authors: Khamto, Nopawit, Utama, Kraikrit, Tateing, Suriya, Sangthong, Padchanee, Rithchumpon, Puracheth, Cheechana, Nathaporn, Saiai, Aroonchai, Semakul, Natthawat, Punyodom, Winita, Meepowpan, Puttinan
• Format: Article
• Language: English
• Subjects: Animals; Antiviral Agents - pharmacology; Benzylisoquinolines - pharmacology; Chlorocebus aethiops; COVID-19; Humans; Molecular Docking Simulation; Molecular Dynamics Simulation; Phytochemicals - pharmacology; Plants, Medicinal - chemistry; Protease Inhibitors; SARS-CoV-2 - drug effects; Vero Cells
• ISSN: 1549-9596; 1549-960X
• DOI: 10.1021/acs.jcim.2c01309

The emergence of SARS-CoV-2 in December 2019 has become a global issue due to the continuous upsurge in patients and the lack of drug efficacy for treatment. SARS-CoV-2 3CL is one of the most intriguing biomolecular targets among scientists worldwide for developing antiviral drugs due to its relevance in viral replication and transcription. Herein, we utilized computer-assisted drug screening to investigate 326 natural products from Thai traditional plants using structure-based virtual screening against SARS-CoV-2 3CL . Following the virtual screening, the top 15 compounds based on binding energy and their interactions with key amino acid Cys145 were obtained. Subsequently, they were further evaluated for protein-ligand complex stability molecular dynamics simulation and binding free energy calculation using molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) approaches. Following drug-likeness and ADME/Tox assessments, seven bisbenzylisoquinolines were obtained, including neferine ( ), liensinine ( ), isoliensinine ( ), dinklacorine ( ), tiliacorinine ( ), 2'-nortiliacorinine ( ), and yanangcorinine ( ). These compounds computationally showed a higher binding affinity than native N3 and GC-373 inhibitors and attained stable interactions on the active site of 3CL during 100 ns in molecular dynamics (MD) simulation. Moreover, the enzymatic assay showed that most bisbenzylisoquinolines could experimentally inhibit SARS-CoV-2 3CL . To our delight, isoliensinine ( ) isolated from demonstrated the highest inhibition of protease activity with the IC value of 29.93 μM with low toxicity on Vero cells. Our findings suggested that bisbenzylisoquinoline scaffolds could be potentially used as an model for the development of effective anti-SARS-CoV-2 drugs.