Discovery of Potential Multi-Target-Directed Ligands by Targeting Host-specific SARS-CoV-2 Structurally Conserved Main Protease^$.

Joshi RS, Jagdale SS, Bansode SB, Shankar SS, Tellis MB, Pandya VK, Chugh A, Giri AP, Kulkarni MJ

10.1080/07391102.2020.1760137

Research curated

Abstract

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 are going on in the drug discovery to control the SARS-CoV-2 viral infection. The main protease (MPro) plays a critical role in viral replication and maturation, thus can serve as the primary drug target. To understand the structural evolution of MPro, we have performed phylogenetic and Sequence Similarity Network analysis, that depicted divergence of Coronaviridae MPro in five clusters specific to viral hosts. This clustering was corroborated with the comparison of MPro 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 MPro. 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 MPro 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 MPro. 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.

Source: PubMed

Related molecules

Name	Synonyms	Genes
delta-viniferin
chrysanthemin
Taiwanhomoflavone A
Nympholide A
Myricitrin	Myricetin, Cannabiscetin, MYC, Myricetin, Myricetol
RNA dependent RNA polymerase	RDR, viral RNA polymerase, RdRp, nsp12	rep, ORF1a-1b, RdRp
Saquinavir
3C-like protease	3CLpro, Mpro, SARS coronavirus main peptidase, 3CLpro-SARS-CoV-2	rep, ORF1a-1b

Related interactions

Target	Drug	Type	Result
3C-like protease	delta-viniferin	Computational	positive
3C-like protease	chrysanthemin	Computational	positive
RNA dependent RNA polymerase	delta-viniferin	Computational	positive
3C-like protease	Taiwanhomoflavone A	Computational	positive
RNA dependent RNA polymerase	Taiwanhomoflavone A	Computational	positive
3C-like protease	Nympholide A	Computational	positive
RNA dependent RNA polymerase	Nympholide A	Computational	positive
3C-like protease	Myricitrin	Computational	positive
RNA dependent RNA polymerase	Saquinavir	Computational	positive
RNA dependent RNA polymerase	Myricitrin	Computational	positive
3C-like protease	Saquinavir	Computational	positive