molecular dynamics simulation

Computer-directed rational engineering of dioxygenase TcsAB for triclosan biodegradation under cold conditions

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Scientists engineered a special enzyme called TcsAB to work better at cold temperatures, enabling it to break down triclosan, a harmful antibacterial chemical that pollutes our water. By using computer simulations and strategic mutations, they created a modified enzyme that degrades triclosan 2.5 times more efficiently at 15°C. When inserted into bacteria, this engineered enzyme helps clean up triclosan pollution in natural environments without requiring energy-intensive heating.

Silk-based microparticles for the adsorption of methylene blue: formulations, characterization, adsorption study, in silico molecular docking, and molecular dynamics simulation

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This research demonstrates that microparticles made from silk fibroin, a protein derived from silkworm cocoons, are exceptionally effective at removing methylene blue dye from water. The silk-based particles work about 32 times better than other forms of silk and can absorb large amounts of the toxic dye. Scientists used computer simulations to understand exactly how the silk protein attracts and binds the dye molecules, providing insights for creating even better eco-friendly water treatment materials.

Molecular docking as a tool for the discovery of molecular targets of nutraceuticals in diseases management

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This review explains how scientists use computer simulations to understand how natural food compounds (called nutraceuticals) interact with disease-causing molecules in the body. By using molecular docking software, researchers can predict which compounds might fight diseases like cancer and heart disease before conducting expensive laboratory tests. The review shows that many common foods like turmeric, grapes, and green tea contain compounds that could potentially treat various diseases by targeting specific proteins and pathways involved in disease development.

Decoding of novel umami-enhancing peptides from Hericium Erinaceus and its mechanisms by virtual screening, multisensory techniques, and molecular simulation approaches

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Researchers discovered four special proteins (peptides) from lion’s mane mushrooms that can enhance the savory umami taste of foods while potentially allowing for less salt in products. These peptides work by helping salt compounds stick better to taste receptors in your mouth. This discovery could help food companies create healthier products with better flavor but lower sodium content, reducing the health risks associated with excessive salt consumption.

Confirmation-dependent organic phosphor reveals amino acid nanoaggregates in ice with insight for prebiotic chemistry

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Scientists have discovered that when amino acids (the building blocks of proteins) freeze in water ice, they naturally clump together into tiny particles called nanoaggregates. Using a special glowing molecule as a detector, researchers directly observed these clumps for the first time using electron microscopes. This finding suggests that icy environments in space or on early Earth could have naturally concentrated amino acids and created the right conditions for them to link together into proteins, potentially contributing to the origin of life.

Targeting SARS-CoV-2 with Chaga mushroom: An in silico study toward developing a natural antiviral compound

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This study used computer modeling to investigate whether Chaga mushroom components can bind to and potentially block the coronavirus spike protein that SARS-CoV-2 uses to infect cells. The researchers found that three active compounds in Chaga—beta glycan, betulinic acid, and galactomannan—attached strongly to the virus’s binding sites in ways similar to known antiviral molecules. Beyond blocking viral entry, Chaga also has immune-boosting and anti-inflammatory properties that could help prevent the dangerous cytokine storm associated with severe COVID-19.

Ganoderic Acid A targeting leucine-rich repeat kinase 2 involved in Parkinson’s disease–A computational study

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Researchers used computer modeling to test five compounds from Reishi mushrooms against a protein called LRRK2 that is linked to Parkinson’s disease. Ganoderic Acid A showed the strongest binding to this target protein and could potentially be developed into a treatment. The findings suggest that Reishi mushroom compounds may help protect brain cells from the degeneration seen in Parkinson’s disease and warrant further laboratory and animal testing.

Synthesis and biological assessment of novel 4H-chromene-3-carbonitrile derivatives as tyrosinase inhibitors

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Researchers developed new chemical compounds that can block tyrosinase, an enzyme responsible for producing excessive skin pigment that causes dark spots and discoloration. The most effective compound (6f) works better than kojic acid, a commonly used skin-lightening ingredient, and could lead to safer treatments for hyperpigmentation and related skin conditions. Computer simulations showed that one form of the compound fits better into the enzyme’s active site, making it more effective at preventing melanin production.

Synergistic target network construction and dynamic simulation analysis based on a prospective systems pharmacology strategy

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Researchers used computer-based methods to study how Sang Huang, a traditional medicinal fungus, might help treat type 2 diabetes. They identified 17 active compounds in the fungus and found that a key component called estradiol dipropionate could improve insulin sensitivity and glucose control by activating specific protein pathways. The study suggests Sang Huang could be a promising natural treatment for diabetes, though more laboratory and animal testing is needed.

In silico screening and molecular dynamics analysis of natural DHPS enzyme inhibitors targeting Acinetobacter baumannii

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Researchers used computer modeling to find natural compounds from plants and mushrooms that can inhibit a key bacterial enzyme (DHPS) in dangerous antibiotic-resistant bacteria called Acinetobacter baumannii. They tested thousands of natural molecules and identified two promising candidates that bind strongly to this enzyme and prevent bacteria from producing folic acid, which they need to survive. The study suggests these natural compounds could potentially be developed into new antibiotics to fight infections caused by drug-resistant bacteria.

Research Keyword: molecular dynamics simulation