1. In Silico Identification of Potential Natural Product Inhibitors of Human Proteases Key to SARS-CoV-2 Infection.
- Author
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Vivek-Ananth RP, Rana A, Rajan N, Biswal HS, and Samal A
- Subjects
- Amino Acid Sequence, Antiviral Agents isolation & purification, Antiviral Agents pharmacology, Betacoronavirus pathogenicity, Binding Sites, COVID-19, Cathepsin L antagonists & inhibitors, Cathepsin L genetics, Cathepsin L metabolism, Coronavirus Infections drug therapy, Coronavirus Infections enzymology, Coronavirus Infections virology, Coumarins chemistry, Coumarins isolation & purification, Coumarins pharmacology, Gene Expression, High-Throughput Screening Assays, Host-Pathogen Interactions drug effects, Host-Pathogen Interactions genetics, Humans, India, Molecular Docking Simulation, Molecular Dynamics Simulation, Monosaccharides chemistry, Monosaccharides isolation & purification, Monosaccharides pharmacology, Pandemics, Phytochemicals isolation & purification, Phytochemicals pharmacology, Plants, Medicinal chemistry, Pneumonia, Viral drug therapy, Pneumonia, Viral enzymology, Pneumonia, Viral virology, Protease Inhibitors isolation & purification, Protease Inhibitors pharmacology, Protein Binding, Protein Conformation, alpha-Helical, Protein Conformation, beta-Strand, Protein Interaction Domains and Motifs, Quinazolines chemistry, Quinazolines isolation & purification, Quinazolines pharmacology, Receptors, Virus antagonists & inhibitors, Receptors, Virus genetics, Receptors, Virus metabolism, SARS-CoV-2, Serine Endopeptidases genetics, Serine Endopeptidases metabolism, Thermodynamics, Virus Internalization drug effects, Antiviral Agents chemistry, Betacoronavirus drug effects, Cathepsin L chemistry, Phytochemicals chemistry, Protease Inhibitors chemistry, Receptors, Virus chemistry, Serine Endopeptidases chemistry
- Abstract
Presently, there are no approved drugs or vaccines to treat COVID-19, which has spread to over 200 countries and at the time of writing was responsible for over 650,000 deaths worldwide. Recent studies have shown that two human proteases, TMPRSS2 and cathepsin L, play a key role in host cell entry of SARS-CoV-2. Importantly, inhibitors of these proteases were shown to block SARS-CoV-2 infection. Here, we perform virtual screening of 14,011 phytochemicals produced by Indian medicinal plants to identify natural product inhibitors of TMPRSS2 and cathepsin L. AutoDock Vina was used to perform molecular docking of phytochemicals against TMPRSS2 and cathepsin L. Potential phytochemical inhibitors were filtered by comparing their docked binding energies with those of known inhibitors of TMPRSS2 and cathepsin L. Further, the ligand binding site residues and non-covalent interactions between protein and ligand were used as an additional filter to identify phytochemical inhibitors that either bind to or form interactions with residues important for the specificity of the target proteases. This led to the identification of 96 inhibitors of TMPRSS2 and 9 inhibitors of cathepsin L among phytochemicals of Indian medicinal plants. Further, we have performed molecular dynamics (MD) simulations to analyze the stability of the protein-ligand complexes for the three top inhibitors of TMPRSS2 namely, qingdainone, edgeworoside C and adlumidine, and of cathepsin L namely, ararobinol, (+)-oxoturkiyenine and 3α,17α-cinchophylline. Interestingly, several herbal sources of identified phytochemical inhibitors have antiviral or anti-inflammatory use in traditional medicine. Further in vitro and in vivo testing is needed before clinical trials of the promising phytochemical inhibitors identified here.
- Published
- 2020
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