COVID-19 (coronavirus disease 2019) is a viral respiratory disease spreading throughout the world. It has been declared a public health emergency and a pandemic by the World Health Organization (WHO). A lack of effective therapeutic efforts has hampered the treatment of COVID-19.
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Main protease (MPRO) plays a critical role in the viral replication cycle.
Once inside a host cell, SARS-CoV-2 begins producing non-structural proteins that facilitate replication and spread, among which is the main protease 3-chymotrypsin-like protease (MPRO), responsible for proteolytic processing.
This enzyme demonstrates extreme specificity towards viral polypeptide sequences, interacting with host proteins minimally. This means that any drugs targeting the enzyme are unlikely to also inhibit host proteases, making the essential SARS-CoV-2 enzyme a particularly attractive drug target.
Cyperus rotundus is a plant with a history as herbal medicine, containing many chemical substances frequently found to be drug-like in character: flavonoids, terpenoids, and the like. Compounds sourced from the plant have demonstrated some inhibitory activity against HIV by modulation of the CYP3A4 enzyme, and thus in a drug lead discovery effort, Kumar et al. (July 2021) computationally screened these natural compounds against MPRO in a paper recently published to Computers in Biology and Medicine.
Screening for ligands
A library of 390 compounds sourced from Cyperus rotundus was assembled in silico and checked for drug-likeness, having good bioavailability by the ability to cross membranes, leaving 354 relevant ligands.
7,938 conformers were generated from these ligands, and docking simulations ran against MPRO, based on the crystal structure of the enzyme. The top 30 ranking compounds in terms of LibDock score, which provides a numerical value based on electrostatic interactions between molecules, were carried forward for more detailed testing of binding energy. Compounds that bonded with the MPRO active site with negative binding energy, and therefore provide a stable bond suitable for an inhibitory drug, were selected from the drug leads, leaving 12 compounds of interest.
Lupeol demonstrated the most favorable docking affinity towards MPRO, followed by β-amyrin acetate, achieving scores of -70.03 and -59.33 kcal/mol, respectively. Interestingly, the antiretroviral protease inhibitor drugs lopinavir and ritonavir, shown in some studies to be effective against COVID-19, achieved scores of only -50.25 and -68.58 kcal/mol, respectively. Other compounds showed good binding affinities with MPRO, comparable to these commercial drugs, and so were also selected for further examination: leanolic acid, β-amyrin, stigmasta-5,22-dien-3-ol, and valrenyl acetate. The root mean square deviation of the ligands once bound was also assessed to determine the flexibility of the compounds, with β-amyrin, stigmasta-5,22-dien-3-ol, and valrenyl acetate demonstrating the greatest rigidity. β-amyrin followed by stigmasta-5,22-dien-3-ol had the largest total binding free energy, indicating stronger intermolecular interactions and more stable bonds.
Bioavailability and toxicity
β-amyrin and stigmasta-5,22-dien-3-ol were examined with regards to pharmacokinetics and toxicity, both demonstrating adequate oral bioavailability and exceptional intestinal absorption approaching 100%. They also test highly against blood-brain-barrier and central nervous system permeability, suggesting that they would biodistribute well through both. The drugs do not inhibit human cytochrome P450, indicating that the drugs are not metabolized.
The drug leads were exposed to the Ames toxicity test, exhibiting low toxicity, though scored relatively highly in terms of acute toxicity by considering rat and minnow LD50 values for the compounds. The group suggests that the two drug leads should likely be well tolerated by humans, though this would need to be verified experimentally by in vitro and in vivo studies.
The researchers concluded that Cyperus rotundus Linn. medicinal plant helps treat viral infections in a traditional manner, and that it may be useful in developing novel and effective therapeutics against COVID-19.
- S. Birendra Kumar, Swati Krishna, Sneha Pradeep, Divya Elsa Mathews, Ramya Pattabiraman, Manikanta Murahari, T.P. Krishna Murthy, Screening of natural compounds from Cyperus rotundus Linn against SARS-CoV-2 main protease (Mpro): An integrated computational approach, Computers in Biology and Medicine, https://doi.org/10.1016/j.compbiomed.2021.104524, https://www.sciencedirect.com/science/article/pii/S0010482521003188