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Photodynamic therapy (PDT) is a rapidly evolving area of cancer management against solid tumors. PDT is either administrated by injecting photosensitizer (porphyrins) or by accumulation of intracellular protoporphyrin IX via the inhibition of human Protoporphyrinogen Oxidase IX (hPPO). In this study, novel inhibitors of hPPO have been investigated by integrating virtual screening, molecular docking, and molecular dynamics (MD) simulation. A ligand-based pharmacophore was generated from a training set of 22 inhibitors of hPPO. The selected pharmacophore had four chemical features including three hydrogen bond acceptors and one hydrophobic. The pharmacophore was characterized by highest correlation coefficient of 0.96, cost difference of 53.20, and lowest root mean square deviation of 0.73. The resultant pharmacophore was validated by Fischer's Randomization and Test Set Validation methods. The validated pharmacophore was used as a 3D query to screen chemical databases including NCI, Asinex, Chembridge, and Maybridge. The screening of chemical databases and the subsequent application of Lipinski's Rule of Five , and ADMET Assessment Test , retrieved 1176 drug-like compounds. The drug-like compounds were subjected to molecular docking studies in the active site of hPPO to eliminate false positive hits and to elucidate their true binding orientation. Top three candidate molecules with high docking scores and hydrogen bond interactions with catalytic active residues were selected as best candidate inhibitors against hPPO. The binding stability of selected candidate inhibitors was evaluated by MD simulation. The MD simulation of hits portrayed strong hydrogen bonds and key hydrophobic interactions with catalytic active residues of hPPO including R59, R97, G159, G332 and flavin moiety of FAD (coenzyme of hPPO). Our study predicts three hit compounds against hPPO, which could possibly accumulate high concentration of protoporphyrinogen-IX, and thereby acting as an intracellular photosensitizer against tumor cells through photodynamic therapy. [ABSTRACT FROM AUTHOR]

The pandemic caused by the SARS-CoV-2 virus has claimed more than 6.5 million lives worldwide. This global challenge has led to accelerated development of highly effective vaccines tied to their ability to elicit a sustained immune response. While numerous studies have focused primarily on the spike (S) protein, less is known about the interior of the virus. Here we propose a methodology that combines several experimental and simulation techniques to elucidate the internal structure and mechanical properties of the SARS-CoV-2 virus. The mechanical response of the virus was analyzed by nanoindentation tests using a novel flat indenter and evaluated in comparison to a conventional sharp tip indentation. The elastic properties of the viral membrane were estimated by analytical solutions, molecular dynamics (MD) simulations on a membrane patch and by a 3D Finite Element (FE)-beam model of the virion's spike protein and membrane molecular structure. The FE-based inverse engineering approach provided a reasonable reproduction of the mechanical response of the virus from the sharp tip indentation and was successfully verified against the flat tip indentation results. The elastic modulus of the viral membrane was estimated in the range of 7–20 MPa. MD simulations showed that the presence of proteins significantly reduces the fracture strength of the membrane patch. However, FE simulations revealed an overall high fracture strength of the virus, with a mechanical behavior similar to the highly ductile behavior of engineering metallic materials. The failure mechanics of the membrane during sharp tip indentation includes progressive damage combined with localized collapse of the membrane due to severe bending. Furthermore, the results support the hypothesis of a close association of the long membrane proteins (M) with membrane-bound hexagonally packed ribonucleoproteins (RNPs). Beyond improved understanding of coronavirus structure, the present findings offer a knowledge base for the development of novel prevention and treatment methods that are independent of the immune system. [ABSTRACT FROM AUTHOR]

Abstract Platinum-decorated functionalized graphene sheet (Pt@FGS) is a promising nanoparticle additive for catalytic fuel combustion. In this study, four cases involving pure methane oxidation and methane oxidation in the presence of various Pt/graphene-based nanoparticle catalysts are investigated using the reactive force field molecular dynamics (ReaxFF MD) simulations to reveal catalytic mechanisms and kinetics of methane oxidation. The results demonstrate that Pt@FGS is the most effective catalyst among all the nanoparticle candidates involved in this research. Compared with pure methane oxidation, the combination of Pt and FGS in the Pt@FGS reaction improves the catalytic activity by dramatically lowering the activation energy by approximately 73%. Additionally, the catalytic methane oxidation is initiated by the cleavage of C H bond and the production of hydroxyl. The observed H transfer process suggests that enhanced dehydrogenation of Pt@FGS and interatomic exchanges activate the catalytic cycle and dominate the catalytic process. Moreover, FGS can be further oxidized mostly at the edge of the sheet to increase the functionality. In summary, this research sheds light on the catalytic mechanisms for enhanced fuel combustion in the presence of Pt@FGS. [ABSTRACT FROM AUTHOR]

This paper reveals the influence of easiness of boiling of tool electrode materials on the machining speed in EDM. It is considered that during the discharge process, both the anode and cathode emit the metal vapor jets into the gap. The interaction of the jets in the gap generates a kind of shear force acting on the molten pool, which helps remove the molten material in the workpiece. Moreover, it was found that lower boiling point of tool electrode results in stronger interaction of the jets and larger shear force, thereby the material removal volume of the discharge crater will be larger. To validate the above thoughts, the effect of the interaction of the jets on the material removal process was investigated through the molecular dynamics simulation. Then, the material removal volume of the discharge crater in a series of single discharge experiments using tool electrodes with different thermo-physical properties related to the easiness of boiling was compared to verify the simulation results. Finally, the machining experiments were performed using a sinking EDM machine to verify the higher removal performance of tool electrode materials which are easy to emit vapor jets. [ABSTRACT FROM AUTHOR]

Three-dimensional periodic molecular models of amorphous cis-1,4-polybutadiene ( cis-PBD) were constructed using the Materials Studio (MS)® software to study the effects of temperature on the diffusion of oxygen (O2). The radial distribution function, solubility parameter and others clearly proved the three-dimensional periodic molecular model was able to reproduce bulk experimental data of the authentic materials. The volume fraction of accessible oxygen was reckoned by fractional free volume with a probe radius of 1.8 Å. The diffusion coefficients (D) of O2 were calculated, and researches on the diffusion mechanism were made. Data obtained corresponded with the trend from available experiments and previously published simulation work. The results confirmed the accelerating effect of high temperatures on the diffusion of O2 and meanwhile suggested the favourable binding sites of thermo-oxidative aging reactions. Our findings have an important significance for promoting the development of membrane separation technology and provide valuable guidance for further research on thermo-oxidative aging of cis-PBD. [ABSTRACT FROM AUTHOR]

The phytochemicals can play complementary medicine compared to synthetic drugs considering their natural origin, safety, and low cost. Phytochemicals hold a key position for the expansion of drug development against corona viruses and need better consideration to the agents that have already been shown to display effective activity against various strains of corona viruses. In this study, we performed molecular docking studies on potential forty seven phytochemicals which are SARS-CoV-1 Mpro inhibitors to identify potential candidate against the main proteins of SARS-CoV-2. In Silico Molecular docking studies revealed that phytochemicals 16 (Broussoflavan A), 22 (Dieckol), 31 (Hygromycin B), 45 (Sinigrin) and 46 (Theaflavin-3,3′-digallate) exhibited excellent SARS-CoV-2 Mpro inhibitors. Furthermore, supported by Molecular dynamics (MD) simulation analysis such as Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), Radius of gyration (Rg) and H-bond interaction analysis. We expect that our findings will provide designing principles for new corona virus strains and establish important frameworks for the future development of antiviral drugs. [ABSTRACT FROM AUTHOR]