This work aimed at evaluating the inhibitory effect of ten natural bioactive compounds (1–10) as potential inhibitors of SARS-CoV-2-3CL main protease (PDB ID: 6LU7) and SARS-CoV main proteases (PDB IDs: 2GTB and 3TNT) by molecular docking analysis. The inhibitory effect of all studied compounds was studied with compared to some proposed antiviral drugs which currently used in COVID-19 treatment such as chloroquine, hydroxychloroquine, azithromycin, remdesivir, baloxvir, lopinavir, and favipiravir. Homology modeling and sequence alignment was computed to evaluate the similarity between the SARS-CoV-2-3CL main protease and other SARS-CoV receptors. ADMET properties of all studied compounds were computed and reported. Also, molecular dynamic (MD) simulation was performed on the compound which has the highest binding affinity inside 6LU7 obtained from molecular docking analysis to study it is stability inside receptor in explicit water solvent. Based on molecular docking analysis, we found that caulerpin has the highest binding affinity inside all studied receptors compared to other bioactive compounds and studied drugs. Our homology modeling and sequence alignment showed that SARS-CoV main protease (PDB ID: 3TNT) shares high similarity with 3CLpro (96.00%). Also, ADMET properties confirmed that caulerpin obeys Lipinski’s rule and passes ADMET property, which make it a promising compound to act as a new safe natural drug against SARS-CoV-2-3CL main protease. Finally, MD simulation confirmed that the complex formed between caulerpin and 3CLpro is stable in water explicit and had no major effect on the flexibility of the protein throughout the simulations and provided a suitable basis for our study. Also, binding free energy between caulerpin and 6LU7 confirmed the efficacy of the caulerpin molecule against SARS-CoV-2 main protease. So, this study suggested that caulerpin could be used as a potential candidate in COVID-19 treatment.
1 September 2020 in Journal of Biomolecular Structure and Dynamics
In this work, the ability of B12N12 fullerene-like nanoclusters as a drug carrier for isoniazid anti-tuberculosis drug has been studied by DFT methods. Binding energies in both gas and water phases are reported. The formed bonds between B12N12-FLN and Iso drug are studied and computed using QMAIM method. NPA is computed to obtain the total charges transferred in the B12N12-FLN-Iso drug complexes, NPA obtained values suggested that the cluster may oxidize the coordinated of Iso drug. The charge-transfer energy values are also computed and confirmed that the charges were transferred from the non-bonding lone-pair (n) of N and O atoms orbitals to the σ* orbitals of B and N atoms of B12N12-FLN. Also, the adsorption of Iso drug on BN nanoparticles surface (different sizes and shapes) and BN nanotubes was studied by Monte Carlo simulation. We found that increasing the BN size did not affect significantly on the adsorption energies of Iso drug for all various BN nanoparticles shapes. All adsorption energies obtained by MC calculations are negative values which revealed that the adsorption of the Iso drug molecule on BN surfaces is exothermic, spontaneous and energetically favourable. Also, the stability of B12N12-FLN-Iso drug complex in water explicitly was studied by MD simulations. MD simulation confirmed that iso-B12N12-FLN complexes are stable in the presence of water molecules. So, finally, we deduced that B12N12 fullerene-like nanoclusters can be acted as a drug carrier for isoniazid anti-tuberculosis drug. Communicated by Ramaswamy H. Sarma
A dependent step-by-step study that included experimental and field study was applied to explore the simplest and most effective system that could be applied for adsorption of Congo Red (CR) dye from the effluent of wastewater that comes out from different industries. Zeolite (Z) surface and pores were subjected to a modification process using green seaweed (GS) algae. Thereafter, each Z, GS, and composite from both were evaluated based on the adsorption efficacy to clean up CR dyes from aqueous solutions. A wet impregnation method was followed to fabricate the zeolite/algae (ZGS) nanocomposite which was characterized using the most appropriate characterization techniques. Batch experiments were selected to be the method of choice in order to follow up the performance of the adsorption process versus different practical variables. Moreover, dye adsorption kinetics and isotherms were investigated as well. At lowered concentrations of CR, the novel nanocomposite ZGS revealed more efficacy than its counterparts, Z and GS, in terms of the adsorption capacity. The maximum adsorption capacities were found to be 8.10, 10.30, and 19.70 mg/g for Z, GS, and ZGS, respectively. Laboratory tests confirmed that the novel nanocomposite ZGS could be introduced as a new and economical nanoadsorbent to capture and remove negatively charged dyes from wastewater effluents that come out from industries at lower concentrations of CR dye and analogous compounds. The dye adsorption on GS, Z, and ZGS coincide with the pseudo-first, Langmuir isotherm, and second-order models. Evaluation for the sorption mechanism was conducted using a diffusion model known as Weber’s intraparticle. Depending on the last findings, field experiments on removing dyes from industrial wastewater revealed optimistic findings as the efficiency of our modern and eco-friendly nanoadsorbent reached 91.11%, which helps in the reuse of industrial wastewater.