Exploring the Binding Interaction of Active Compound of Pineapple against Foodborne Bacteria and Novel Coronavirus (SARS-CoV-2) Based on Molecular Docking and Simulation Studies

Abstract

Natural resources, particularly plants and microbes, are an excellent source of bioactive molecules. Bromelain, a complex enzyme mixture found in pineapples, has numerous pharmacological applications. In a search for therapeutic molecules, we conducted an in silico study on natural phyto-constituent bromelain, targeting pathogenic bacteria and viral proteases. Docking studies revealed that bromelain strongly bound to food-borne bacterial pathogens and SARS-CoV-2 virus targets, with a high binding energy of −9.37 kcal/mol. The binding interaction was mediated by the involvement of hydrogen bonds, and some hydrophobic interactions stabilized the complex and molecular dynamics. Simulation studies also indicated the stable binding between bromelain and SARS-CoV-2 protease as well as with bacterial targets which are essential for DNA and protein synthesis and are required to maintain the integrity of membranous proteins. From this in silico study, it is also concluded that bromelain could be an effective molecule to control foodborne pathogen toxicity and COVID-19. So, eating pineapple during an infection could help to interfere with the pathogen attaching and help prevent the virus from getting into the host cell. Further, research on the bromelain molecule could be helpful for the management of COVID-19 disease as well as other bacterial-mediated diseases. Thus, the antibacterial and anti-SARS-CoV-2 virus inhibitory potentials of bromelain could be helpful in the management of viral infections and subsequent bacterial infections in COVID-19 patients.

Investigating the Antiviral Properties of Nyctanthes arbor-tristis Linn against the Ebola, SARS-CoV-2, Nipah, and Chikungunya Viruses: A Computational Simulation Study

“…The 2D conformational information, including SMILES IDs, of the most significant 26 natural compounds of the plant N. arbor-tristis and control drug remdesivir was downloaded from the PubChem database [32] and utilized by converting it into 3D structural files for further molecular docking and simulation purposes. Furthermore, generated ligand files were submitted to the Discovery Studio Visualizer version 24.1.0.23298 for the energy minimization process using the CHARMm forcefield [33], which signifies the functional empirical energy to treat macromolecular systems as a model [34][35][36][37].…”

“…These amino acid residues were then considered for docking studies. With the aid of Discovery Studio Visualizer version 24.1.0.23298, PDB files were rendered in 3D [34,35].…”

Computational Approaches to Evaluate the Acetylcholinesterase Binding Interaction with Taxifolin for the Management of Alzheimer’s Disease

“…Where ∆Vdwaals = van der Waals energy; ∆EEL = electrostatic molecular energy; ∆EPB = polar contribution to the solvation energy; ∆ENPOLAR = nonpolar contribution of repulsive solute-solvent interactions to the solvation energy; ∆EDISPER = nonpolar contribution of attractive solute-solvent interactions to the solvation energy; ∆GGas = total gas phase molecular energy; ∆GSolv = total solvation energy; and ∆GTotal = total binding energy. [23,24].…”

Computational Molecular Docking and Simulation-Based Assessment of Anti-Inflammatory Properties of Nyctanthes arbor-tristis Linn Phytochemicals

“…We then used the Novoprolab server (https://www.novoprolabs.com/tools/smiles2pdb) (accessed on 12 October 2023) to convert the SMILES IDs into 3D PDB files [37] for subsequent molecular docking and simulation studies. Next, we submitted the ligand files to Discovery Studio Visualizer version 21.1.0.20298 for the energy minimization [38]. We applied the CHARMm force field to model the macromolecular systems using the empirical energy functions [39,40].…”