A threefold approach including quantum chemical, molecular docking and molecular dynamic studies to explore the natural compounds from Centaurea jacea as the potential inhibitors for COVID-19

Abstract

In the current report, we studied the possible inhibitors of COVID-19 from bioactive constituents of Centaurea jacea using a threefold approach consisting of quantum chemical, molecular docking and molecular dynamic techniques. Centaurea jacea is a perennial herb often used in folk medicines of dermatological complaints and fever. Moreover, anticancer, antioxidant, antibacterial and antiviral properties of its bioactive compounds are also reported. The Mpro (Main proteases) was docked with different compounds of Centaurea jacea through molecular docking. All the studied compounds including apigenin, axillarin, Centaureidin, Cirsiliol, Eupatorin and Isokaempferide, show suitable binding affinities to the binding site of SARS-CoV-2 main protease with their binding energies -6.7 kcal/mol, -7.4 kcal/mol, -7.0 kcal/mol, -5.8 kcal/mol, -6.2 kcal/mol and -6.8 kcal/mol, respectively. Among all studied compounds, axillarin was found to have maximum inhibitor efficiency followed by Centaureidin, Isokaempferide, Apigenin, Eupatorin and Cirsiliol. Our results suggested that axillarin binds with the most crucial catalytic residues CYS145 and HIS41 of the Mpro, moreover axillarin shows 5 hydrogen bond interactions and 5 hydrophobic interactions with various residues of Mpro. Furthermore, the molecular dynamic calculations over 60 ns (6×106 femtosecond) time scale also shown significant insights into the binding effects of axillarin with Mpro of SARS-CoV-2 by imitating protein like aqueous environment. From molecular dynamic calculations, the RMSD and RMSF computations indicate the stability and dynamics of the best docked complex in aqueous environment. The ADME properties and toxicity prediction analysis of axillarin also recommended it as safe drug candidate. Further, in vivo and in vitro investigations are essential to ensure the anti SARS-CoV-2 activity of all bioactive compounds particularly axillarin to encourage preventive use of Centaurea jacea against COVID-19 infections.

Graphene oxide and flavonoids as potential inhibitors of the spike protein of SARS-CoV-2 variants and interaction between ligands: a parallel study of molecular docking and DFT

“…Studies show that the proposal of a GO-based nanocarrier doped with molecules via π-π bonding, as pointed out in this work, is successfully carried out [41]. The therapeutic activities of the chosen biomolecules are pointed out in the literature; however, it is noteworthy that new molecular docking studies [55][56][57] and subsequent in vitro tests should be performed to analyze the interaction of the system with the target proteins of SARS-CoV-2, as a proposed treatment against COVID-19.…”

Learning experiences of mathematical situations in university students from the innovation project

“…The development of the Innovation Project is a parallel experience during the development of mathematical content in sixteen weeks. The semantic network shown detected nodes, representing main components of the experiment such as 1) exploring, at this stage, the group of students detected the contextualized problem with a possible solution from the mathematical content (Pisula et al, 2021;Stott, 1973), the specific solution associated with concepts and rules, procedures, Mathematical formulas lead to the next feasibility, in addition, emotions are released, the desire to identify and know the procedures to be developed, frequently answer the questions : will it be a novel solution?, will it allow its practical application?, the solution detected, allows new proposals for entrepreneurs?, these questions and expectations respond to the detachment of the second component 2) define, in this scenario, the challenges are concretized, the unprecedented actions, who carried it out in specific situations raised in the first moment of the exploration , the mathematical concepts are assumed for their applicability that allows its development by associating the exercises and problems raised in the sessions and their applicability (Chun et al, 2020; Muhammad et al, 2021).…”

Quantum Chemical Studies on SARS-CoV-2-a Review

“…Inhibitors are the substances that suppress the activity of another substance. The activity against SARS-CoV-2 of the bio active element of Centaurea jacea has been studied by using a threefold approach and found that it can be used as a preventive measure and found to be a potential inhibitor against COVID-19 infections [4].…”