Discovery of potential multi-target-directed ligands by targeting host-specific SARS-CoV-2 structurally conserved main protease

• Published in: Journal of biomolecular structure & dynamics Vol. 39; no. 9; pp. 3099 - 3114
• Main Authors: Joshi, Rakesh S., Jagdale, Shounak S., Bansode, Sneha B., Shankar, S. Shiva, Tellis, Meenakshi B., Pandya, Vaibhav Kumar, Chugh, Anita, Giri, Ashok P., Kulkarni, Mahesh J.
• Format: Journal Article
• Language: English
• Published: England Taylor & Francis 13-06-2021
• Subjects: Coronavirus; COVID-19; hACE-2; Humans; Ligands; MPro; multi-target-directed ligand; Pandemics; Peptide Hydrolases; Pharmaceutical Preparations; Phylogeny; protease inhibitor; Protease Inhibitors - pharmacology; RdRp; SARS-CoV-2; SARS-CoV-2 virus; COVID-19; protease inhibitor; Coronavirus; MPro; RdRp; SARS-CoV-2 virus; hACE-2; multi-target-directed ligand
• ISSN: 0739-1102; 1538-0254; 1538-0254
• DOI: 10.1080/07391102.2020.1760137

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has resulted in the current COVID-19 pandemic. Worldwide this disease has infected over 2.5 million individuals with a mortality rate ranging from 5 to 10%. There are several efforts going on in the drug discovery to control the SARS-CoV-2 viral infection. The main protease (M
Pro
) plays a critical role in viral replication and maturation, thus can serve as the primary drug target. To understand the structural evolution of M
Pro
, we have performed phylogenetic and Sequence Similarity Network analysis, that depicted divergence of Coronaviridae M
Pro
in five clusters specific to viral hosts. This clustering was corroborated with the comparison of M
Pro
structures. Furthermore, it has been observed that backbone and binding site conformations are conserved despite variation in some of the residues. These attributes can be exploited to repurpose available viral protease inhibitors against SARS-CoV-2 M
Pro
. In agreement with this, we performed screening of ∼7100 molecules including active ingredients present in the Ayurvedic anti-tussive medicines, anti-viral phytochemicals and synthetic anti-virals against SARS-CoV-2 M
Pro
as the primary target. We identified several natural molecules like δ-viniferin, myricitrin, taiwanhomoflavone A, lactucopicrin 15-oxalate, nympholide A, afzelin, biorobin, hesperidin and phyllaemblicin B that strongly binds to SARS-CoV-2 M
Pro
. Intrestingly, these molecules also showed strong binding with other potential targets of SARS-CoV-2 infection like viral receptor human angiotensin-converting enzyme 2 (hACE-2) and RNA dependent RNA polymerase (RdRp). We anticipate that our approach for identification of multi-target-directed ligand will provide new avenues for drug discovery against SARS-CoV-2 infection.
Communicated by Ramaswamy H. Sarma