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The study of the corrosion inhibition of mild steel in acid medium 1 M HCl by the Schiff base compounds named {4,4′-Bis(pyrrole-2-carboxaldehyde) diphenyl diimino sulfide (L1) and 4,4′-Bis(thiophene-2-carboxaldehyde) diphenyl diimino sulfide (L2)} was carried out using various techniques: weight loss measurements, polarization curves, electrochemical impedance spectroscopy (EIS), atomic force microscopy (AFM), Scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS). The influence of the concentration, immersion time and temperature was examined and the mode of adsorption of these inhibitors on the surface of the metal was highlighted by assigning the appropriate isotherm. The experimental results indicate that these compounds are effective corrosion inhibitors and the inhibitory competence rises with increasing inhibitor concentration. The adsorption of these compounds on the mild steel surface obeys the isotherm of Langmuir. The correlation between the molecular structures and the inhibitory properties of the compounds studied was performed using the Density Functional Theory (DFT) method. Furthermore, molecular dynamics (MD) simulation has been taken into account. The results indicate that the adsorption energy of L1 was less than L2, which is in accordance with the experimentally determined inhibition effect.

Molecular dynamics (MD) method was used to simulate the interaction between water-soluble polymers, such as polyacrylic acid (PAA), polymethylacrylic acid (PMAA), acrylic acid-methylacrylate copolymer (AA-MAE), acrylic acid-hydroxypropyl acrylate copolymer (AA-HPA), hydrolyzed polymaleic anhydride (HPMA), acrylic acid-maleic acid copolymer (AA-MA), and hydroxyapatite crystal. The sequence of binding energies of polymers binding with the (100) crystal surface of hydroxyapatite was as follows: AA-HPA > AA-MA > HPMA > PAA > AA-MAE > PMAA. After analyzing various energy components and pair correlation functions of all systems, it could be concluded that binding energies were mainly determined by Coulomb interaction. Polymers deformed during their combining with the hydroxyapatite crystal, but all the deformation energies were far less than respective nonbond energies. The dynamics behavior of carboxyls located at different positions of the polymer chains manifested different features during the processes of MD runs. Carboxyls at the ends of the polymer chains oscillated more acutely than those in the middle of the chains; therefore, the latter ones inhibited scale crystal growth more effectively than the former ones because they combined with hydroxyapatite crystal more firmly.

Chignolin is an artificially designed ten-residue (GYDPETGTWG) folded peptide, which is the smallest protein and provides a good template for protein folding. In this work, we completed four explicit water molecular dynamics simulations of Chignolin folding using GROMOS and OPLS-AA force fields from extended initial states without any experiment informations. The four-folding free energy landscapes of the peptide has been drawn. The folded state of Chignolin has been successfully predicated based on the free energy landscapes. The four independent simulations gave similar results. (i) The four free energy landscapes have common characters. They are fairly smooth, barrierless, funnel-like and downhill without intermediate state, which consists with the experiment. (ii) The different extended initial structures converge at similar folded structures with the lowest free energy under GROMOS and OPLS-AA force fields. In the GROMOS force field, the backbone RMSD of the folded structures from the NMR native structure of Chignolin is only 0.114 nm, which is a stable structure in this force field. In the OPLS-AA force field, the similar results have been obtained. In addition, the smallest RMSD structure is in better agreement with the NMR native structure but unlikely stable in the force field.

Upregulation of MAPK pathway receptors has been majorly reported for the accumulation of tumor cells in non-small cell lung cancer (NSCLC) patients. Several scientific endeavors were committed to developing checkpoint inhibitors for MAPK intermediates. However, poor toxicity profiling and over-expression of other kinases diminish the treatment outcomes. Recently, dual-action drugs are developed to overcome the ineptness and drug resistance that typically occur when the usage of individual checkpoint inhibitors. Therefore, we screened 1574 natural compounds from the NPACT database using high-end computational tools against these attractive kinase targets (RAF and MEK). Initially, Glide docking and prime-MM/GBSA analysis yielded a total of seven hit compounds that showed better binding potency on both targets. The van der Waals interaction energy highly favors the binding of the compound with respective target receptors. Later, we used dynamics ensembles to examine the essential and stable interactions in the complex structures through 16 different MD simulations (50ns) cumulatively in both RAF and MEK systems. These extensive MD analyses resulted in two lead compounds such as NPACT00282 and NPACT01075 having the potential to make a stable complex with RAF and MEK receptors. Notably, the interaction of compounds with CYS532 and TYR125 in RAF and MEK, respectively, might play a crucial role in the compound’s binding process. Furthermore, these lead compounds exhibited good pharmacokinetic/dynamic characteristics. Collectively, we believe that these lead compounds are able to provide better therapeutic options and thus overcome the shortcomings in lung cancer treatment.

Amyloid $\beta$ (A$\beta$) peptide monomers polymerize to form insoluble amyloid fibril aggregates and accumulate as senile plaques which eventually leads to cognitive impairment. Modulating abnormal amyloid aggregation can be considered a therapeutic target for Alzheimer’s disease. Recent studies support that Curcumin interferes with larger protein aggregate formation by destabilizing the salt bridge (Asp 23-Lys 28) of A$\beta$ protein. The chemical library of curcumin derivative with pyrazole, isoxazole, and isothiazole showed considerable binding affinity comparable to that of curcumin. In silico docking studies of the library of the compound, revealed strong binding affinity with A$\beta$ protein and $\beta$-secretase enzyme (BACE1). De novo ligand design coupled with manual pharmacophore mapping of our best-fitting lead revealed another ligand having a potential binding affinity with both A$\beta$ protein and BACE-1. Both the compounds passed Lipinski’s Rule of Five, in silico toxicity testing by admetSAR, and pharmacophore overlaps with Verubecestat, a compound under clinical trial against Alzheimer’s disease. MD dynamic simulation study revealed the stability of protein after it binds to our ligand. Secondary structure determination was also done to observe the changes in $\alpha$ and $\beta$ sheets of the protein with and without ligand binding. Ligand-based drug design was also carried out via pharmacophore mapping and searching the molecules via zinc database.

Nano Fe₄N powder has been successfully prepared by the combination between high pressure combined method of reduction and nitriding and molecular dynamics (MD) simulation. The phase, composition, morphology, and magnetic properties have been preliminarily characterized by XRD, TEM, and VSM to investigate the influence of temperature, time, ammonia hydrogen ratio, and pressure during reaction process on the preparation. The results indicate that the preferable nano Fe₄N powder of the average size around 35nm could be obtained nitriding at 0.4MPa and 673K for 2.5hours with the ammonia hydrogen ratio being 3:1. The results of magnetic detection show that the nano Fe₄N produced here is a fairly desirable soft magnetic material with Ms$=$169.70emu/g. This process could reduce the reaction temperature and shorten the reaction time, which is of important significance to the industrial production of nano Fe₄N powder.

Fungal infection of invasive nature is an alarming threat globally and a leading cause of human morbidity and mortality as they are opportunistic in nature. Rising resistance to current clinically approved marketed products for fungal infections is a major concern for humans. Dihydrofolate Reductase (DHFRase) is an essential enzyme in folate metabolic pathway responsible for DNA synthesis and is ubiquitous to all organisms, and also acts as a key target for developing antifungal drugs. In this study, potential mutant DHFRase inhibitors were screened with the help of hierarchical mode of docking of virtual library of antifungal compounds and molecular dynamic (MD) simulation. The identification of best hits was done by using the docking, binding energy prediction and further, which was supported by their predicted pharmacokinetics. MD simulation of the human DHFRase enzyme with the reference lead compound i.e. PY957 and most promising hit found i.e. ChemDiv-C390-0455 and to validate the stability of enzyme-ligand complex in best 07 retrieved hit as a potential mutant DHFRase inhibitor. The key residues Glh30, Phe34, Phe64, Phe31 of the binding pocket acknowledged as essential were found to be matching with the key interactions of the selected hit. Computed root mean square deviation (RMSD) and root mean square fluctuation (RMSF) in MD simulation of complex of DHFRase enzyme with PY957 and ChemDiv-C390-0455 were read less than 2.25Å during 100 nanoseconds simulation for both complex.