A molecular dynamics simulations analysis of repurposing drugs for COVID-19 using bioinformatics methods.

A number of multidisciplinary methods have piqued the interest of researchers as means to accelerate and lower the cost of medication creation. The goal of this research was to find target proteins and then select a lead drug against SARS-CoV-2. The three-dimensional structure is taken from the RCSB PDB using its specific PDB ID 6lu7. Virtual screening based on pharmacophores is performed using Molecular Operating Environment software. We looked for a potent inhibitor in the FDA-approved database. For docking, AutoDock Vina uses Pyrx. The compound-target protein binding interactions were tested using BIOVIA Discovery Studio. The stability of protein and inhibitor complexes in a physiological setting was investigated using Desmond's Molecular Dynamics Simulation (MD simulation). According to our findings, we repurpose the FDA-approved drugs ZINC000169677008 and ZINC000169289767, which inhibit the activity of the virus's main protease (6lu7). The scientific community will gain from this finding, which might create new medicine. The novel repurposed chemicals were promising inhibitors with increased efficacy and fewer side effects.Communicated by Ramaswamy H. Sarma.

Identification of lead compound screened from the natural products atlas to treat renal inflammasomes using molecular docking and dynamics simulation.

One of the most prevalent ailments is kidney disease. Effective therapies for chronic renal disease are hard to come by. As a result, there is significant clinical and social interest to predict and develop novel compounds to treat renal disorders. So, specific natural products have been employed in this study because they have protective effects against kidney diseases. When taken orally, natural products can help protect against or lessen the severity of the kidney damage caused by high fructose intake, a high-fat diet, and both Type I and Type 2 diabetes. Reduced podocyte injury, a contributor to albuminuria in diabetic nephropathy, reduces renal endothelial barrier function disruption due to hyperglycemia, as well as urinary microalbumin excretion and glomerular hyperfiltration. Multiple natural products have been shown to protect the kidneys from nephrotoxic chemicals such as LPS, gentamycin, alcohol, nicotine, lead, and cadmium, all of which can persuade acute kidney injury (AKI) or chronic kidney disease (CKD). Natural compounds inhibit regulatory enzymes for controlling inflammation-related diseases. For this, use computational methods such as drug design to identify novel flavonoid compounds against kidney diseases. Drug design via computational methods gaining admiration as a swift and effective technique to identify lead compounds in a shorter time at a low cost. In this in-silico study, we screened The Natural Product Atlas based on a structure-based pharmacophore query. Top hits were analyzed for ADMET analysis followed by molecular docking and docking validation. Finally, the lead compound was simulated for a period of 200 ns and trajectories were studied for stability. We found that NPA024823 showed promising binding and stability with the AIM2. This research work aims to predict novel anti-inflammatory compounds against kidney diseases to inhibit kidney inflammasome by targeting the AIM2 protein. So, in initial preclinical research, there will be lower failure rates that demonstrate safety profiles against predicted compounds.Communicated by Ramaswamy H. Sarma.

Graphene oxide-based materials for efficient removal of heavy metal ions from aqueous solution: A review.

Graphene with atomic layer of sp2-hybridized carbon atoms in a hexagonal structure has attracted multidisciplinary attention since its discovery. Due to the inherent advantages of large specific surface area and abundant functional groups, its derivative graphene oxide (GO) nanomaterials have achieved large-scale development in effective pollution treatment. In the past few years, novel GO-based nanomaterials through coupling with other nanomaterials have been synthesized with significant process and applied for efficient elimination of different kinds of pollutants. This paper aims to summarize recent research results on the excellent removal ability of GO-based nanomaterials for various heavy metal ions in aqueous solutions. The synthesis, adsorption process characteristics and interaction mechanism of the adsorbent are emphasized and discussed. The effects of various environmental conditions are outlined. At last, a brief summary, perspective and outlook are presented. This review is intended to provide some thrilling information for the design and manufacture of GO-based nanomaterials for the elimination of heavy metal ions from wastewater in environmental pollution management.

Recent advances in layered double hydroxide-based nanomaterials for the removal of radionuclides from aqueous solution.

Layered double hydroxides (LDHs), one of the most important two-dimensional layered compounds, have enabled massive developments in effective pollution treatments. Their derivative materials have also attracted multidisciplinary attention owing to the intrinsic advantages of their moderate chemiostability, low cost and nontoxicity. Over the past few decades, significant advances have been made in the synthesis of novel LDH-based composites and the optimization of characterization techniques. In this review, we give an overview of the recent advances in LDH-based nanomaterials, from a brief introduction to their preparation and modification methods to an overview of their application in the removal of radionuclides and an exploration of their underlying adsorption mechanisms. In the end, a summary and outlook are also briefly addressed. This review intends to provide deep insight into the design of high-performance LDH-based materials for the potential elimination of radionuclides from aqueous solutions during environmental pollution cleanup.

A novel magnetite nanorod-decorated Si-Schiff base complex for efficient immobilization of U(vi) and Pb(ii) from water solutions.

A novel silicon Schiff base complex (Si-SBC) and magnetite nanorod-decorated Si-SBC (M/SiO2-Si-SBC) were synthesized and well characterized in detail. The synthesized materials were applied for the removal of U(vi) and Pb(ii) from water solutions under various experimental conditions. The monolayer maximum adsorption capacities of M/SiO2-Si-SBC (6.45 × 10-4 mol g-1 for Pb(ii) and 4.82 × 10-4 mol g-1 for U(vi)) obtained from the Langmuir model at 25 °C and pH = 5.00 ± 0.05 were higher than those of Si-SBC (5.18 × 10-4 mol g-1 for Pb(ii) and 3.70 × 10-4 mol g-1 for U(vi)). Moreover, DFT calculations showed that the high adsorption energies (Ead) of 7.61 kcal mol-1 for Pb2+-(Si-SBC) and 2.72 kcal mol-1 for UO22+-(Si-SBC) are mainly attributed to stronger electrostatic interactions. The results revealed that the Si-SBC and M/SiO2-Si-SBC could be used as efficient adsorbents for the effective elimination of U(vi) and Pb(ii) from contaminated wastewater. High sorption capacity and reusability indicated the practical applications of the synthesized materials in environmental pollution cleanup.