A Comparison of Structure, Stability of Neutral and Cationic Vanadium-doped Germanium Clusters GenV0/+ (n = 2 - 8) by using Density Function Theorym clusters GenV0/+ (n = 2 - 8) by using density function theory

The geometries, stabilities and electronic properties of vanadium-doped germanium clusters GenV0/+ (n=2-8) were systematically investigated by using density functional theory (DFT) at the PBE level and the 6-311+G(d) basis set. The results show that the geometries of lowest-energy structures of the cationic clusters are only significant different from those of the neutral at n = 6 or 7. The ground state of neutral clusters is a doublet, except Ge2V which is a quartet while that of cationic clusters is a triplet, except Ge8V+, which is a singlet. The average binding energy values generally increase with increasing cluster size. The results from average binding energies showed that it is more stable for the cationic than neutral clusters at the same size. Furthermore, the calculated values of fragmentation energy, second-order energy difference, HOMO-LUMO gap and adiabatic ionization potential suggest that the neutral clusters possess higher stability when n = 2, 5, 8 and the cations are more stable when n = 2, 3, 5 and 6.

Complexation of 26-Mer Amylose with Egg Yolk Lipids with Different Numbers of Tails Using a Molecular Dynamics Simulation

A molecular dynamics simulation of mixtures of 26-mer amylose with three different egg yolk lipids, namely, cholesterol, triglyceride and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), demonstrated the formation of a stable complex. The 26-mer amylose fluctuated between a coiled and an extended helical conformation. The complex was a V-type amylose complex, with the hydrophobic tail of the lipids being inside the hydrophobic helical cavity of the amylose. The number of glucose units per turn was six for the two helical regions of the amylose-POPC complex and the palmitoyl tail region of the amylose-triglyceride complex. This value was eight for the cholesterol and the two-tail helical region in the amylose-triglyceride complex. Two tails of the POPC were in two different hydrophobic helical regions of the 26-mer amylose, whereas the palmitoyl tail of the triglyceride lay in one hydrophobic helical region and the linoleoyl and oleoyl tails both lay in another helical region, and the cross-sectional area of the latter was larger than the former to accommodate the two tails. The radii of the gyration of the complex were lower for all three cases compared to that of one single amylose. In addition, the stability of the complexes was ranked in the following order: POPC < cholesterol < triglyceride, with their average binding energy being −97.83, −134.09, and −198.35 kJ/mol, respectively.

Elucidation of Teicoplanin Interactions with Drug Targets Related to COVID-19

Teicoplanin is a glycopeptide antibiotic effective against several bacterial infections, has exhibited promising therapeutic efficiency against COVID-19 in vitro, and the rationale for its use in COVID-19 is yet to be recognized. Hence, in this study a number of molecular modeling techniques were employed to decrypt the mechanistic insight of teicoplanin interaction with several COVID-19 drug targets. Initially, molecular docking was employed to study the teicoplanin interaction with twenty-five SARS-CoV-2 structural and non-structural proteins which was followed by molecular mechanics/generalized Born surface area (MM/GBSA) computation for binding energy predictions of top ten models from each target. Amongst all macromolecular targets, the N-terminal domain of the nucleocapsid protein displayed the strongest affinity with teicoplanin showing binding energies of −7.4 and −102.13 kcal/mol, in docking and Prime MM/GBSA, respectively. Thermodynamic stability of the teicoplanin-nucleocapsid protein was further probed by molecular dynamics simulations of protein–ligand complex as well as unbounded protein in 100 ns trajectories. Post-simulation MM-GBSA computation of 50 frames extracted from simulated trajectories estimated an average binding energy of −62.52 ± 12.22 kcal/mol. In addition, conformational state of protein in complex with docked teicoplanin displayed stable root-mean-square deviation/fluctuation. In conclusion, computational investigation of the potential targets of COVID-19 and their interaction mechanism with teicoplanin can guide the design of novel therapeutic armamentarium for the treatment of SARS-CoV-2 infection. However, additional studies are warranted to establish the clinical use or relapses, if any, of teicoplanin in the therapeutic management of COVID-19 patients.

Structural Stability and Thermodynamic Properties of (Y2O3)n(n=1-15) Clusters Based on Density Functional Theory

The initial configuration of Yttrium oxide clusters (Y2O3)n(n=1-15) was creatively constructed by combining artificial bee colony algorithm with density functional theory. The structures of large and medium-sized yttrium oxide clusters with molecular number greater than 10 were established for the first time, and many new structures that are different from existing research have been obtained. The average binding energy, second-order difference energy, HOMO-LUMO gap, density of states and other properties of the clusters were analyzed. The thermodynamic properties and behavior of nano yttrium oxide clusters at different temperatures and sizes were discussed. Studies have shown that for small-sized clusters, the atomic stacking structure is cage-like, while for medium-sized and large-sized clusters, the composite trapezoidal structure and ellipsoid-like structure are more stable. The nanoclusters tend to be stable as a whole, and the relative stability of the cluster structure is higher when n = 2,4,7,9. The effect of yttrium oxygen atomic orbital on bonding is analyzed. The heat capacity (Cp), enthalpy change (H) and entropy (S) of (Y2O3)n (n=1-15) clusters increase with the increase of temperature (T), and the vibration free energy (Gv) decreases with the increase of T. The stability of the clusters changes in the temperature range of 300K-500K.

A rational drug designing: What bioinformatics approach tells about the wisdom of practicing traditional medicines for screening the potential of Ayurvedic and natural compounds for their inhibitory effect against COVID-19 Spike, Indian strain Spike, Papain-like protease and Main Protease protein

The new outbreak of Coronavirus disease (COVID-19) has been entitled as a pandemic by W.H.O. It spreads to almost 211 countries due to its contagious nature. There is an urgent need for developing specific therapeutic agents against COVID-19. We have performed virtual screening of 52 ligands; most of which are essential components of traditional Ayurvedic medicine as well as natural compounds and three were standard repurposing drugs against COVID-19 Spike, Indian strain Spike (IS-Spike), PL-Pro and M-Pro to find potential inhibitor effects. Based on the docking results, it is estimated that compounds have a better binding affinity with M-Pro and PL-Pro than Spike as well as IS-Spike so it can be beneficial as therapeutics against COVID-19. We also conclude that the binding affinity of ligands with IS-Spike gets low as compared to Spike so the inhibitory potential of drugs may get weak. Based on the calculation of average binding energy (B.E) with the three targets, Spike, PL-Pro, and M-Pro, we found10 best ligands viz. (1) Punicafolin (2) Emblicanin A (3) Punigluconin (4) Lopinavir (5) Kuwanon X (6) Rutin (7) Lithospermic Acid (8) Phyllanemblinin A (9) Amarogentin and (10) Amaroswerin for inhibition. These ligands may act as potential inhibitors against COVID-19 druggable tri-targets. Network analysis revealed that four ligands out of 10 leading compounds are common in all four different networks (Spike, IS-Spike, PL-Pro, and M-Pro) which come under Phyllanthus emblica. Notably, a compound of Azadirachta indica out of 4 and a single compound of Swertia chirata was found common in all networks. Additionally, a standard drug Lopinavir and a compound of Salvia miltiorrhiza are frequently found in all networks. In principle, it appears plausible that the compounds which are common in the entire network should have more inhibitory potential against COVID19 due to the better binding potential among all targets, thus providing better candidacy for drug development.

A New Class of Scandium Carbide Nanosheet

A new class of two-dimensional scandium carbide nanosheet has been identified by using first-principles density functional theory. It has a primitive cell of Sc3C10, in which there are two pentagonal carbon rings surrounded by one scandium octagon. Being as the precussor of Volleyballene Sc20C60 and ScC nanotubes, the Sc3C10 nanosheet is exceptionally stable. By rolling up this Sc3C10 sheet, a series of stable ScC nanotubes have been obtained. All the nanotubes studied have been found to be metallic. Furthermore, the hydrogen storage capacity of the ScC nanotubes has been explored. The calculated results show that one unit of the (0,3) ScC nanotube can adsorb a maximum of 51 hydrogen molecules, reaching up to a 6.25 wt% hydrogen gravimetric density with an average binding energy of 0.23 eV/H2.

Theoretical study of the geometrical and electronic properties of Be2Mg+ n (n = 1–11) clusters

By using Density Functional Theory (DFT) method at the B3LYP/6-311G level, the structures, stabilities, and electronic properties of cationic Be2Mg+ n (n = 1–11) clusters have been systematically studied. The optimized geometry show that the ground state structures of cationic Be2Mg+ n (n = 1–11) clusters favor 3D structures except n = 1, 2. Furthermore, the average binding energy E b, the second-order energy differences Δ2E, the fragmentation energy Ef and the HOMO-LUMO energy Egap of the ground state of cationic Be2Mg– n (n = 1–11) clusters are calculated, the final results indicate that Be2Mg+6 and Be2Mg+9 clusters have a higher stability than other clusters. Additionally, the NCP, NEC and Mulliken population analysis reveal that the charges in cationic Be2Mg+ n (n = 1–11) clusters transfer from Mg atom to Be atoms, and strong sp hybridizations are presented in Be atoms of Be2Mg+ n clusters. Finally, the polarizability analysis indicates that the nuclei and electronic clouds of clusters are affected by external field with the increase of cluster size.

Screening of Anti-mycobacterial Phytochemical Compounds for Potential Inhibitors against Mycobacterium Tuberculosis Isocitrate Lyase

Conclusion:Phytochemical based anti-mycobacterial compound can further developed into effective drugs against persistence tuberculosis with lesser toxicity and side effects.Results:Docking and MD simulation studies of top hit compounds have identified shinjudilactone (quassinoid), lecheronol A (pimarane) and caniojane (diterpene) as potential MtbICL inhibitors.Methods:Virtual screening, molecular docking and MD simulation study has been integrated for screening of phytochemical based anti-mycobacterial compounds. Docking study of reported MtbICL inhibitors has shown an average binding affinity score -7.30 Kcal/mol. In virtual screening, compounds exhibiting lower binding energy than calculated average binding energy were selected as top hit compounds followed by calculation of drug likeness property. Relationship between experimental IC50 value and calculated binding gibbs free energy of reported inhibitors was also calculated through regression analysis to predict IC50 value of potential inhibitors.Background and Introduction:Tuberculosis (TB) is a leading infectious disease caused by Mycobacterium tuberculosiswith high morbidity and mortality. Isocitrate lyase (MtbICL), a key enzyme of glyoxylate pathway has been shown to be involved in mycobacterial persistence, is attractive drug target against persistent tuberculosis.

The Studies on Structure and Stability of CaBn Clusters

Calcium-boron systems have excellent properties of hardness, strength, and chemical stability, and we studied a series of CaBn clusters to investigate their structures and relative stability. The results showed the most stable structures of CaBn clusters are not planar. The B atoms tend to get together and form the planar ring to stabilize the structure, and the Ca atoms are coordinated to the periphery of the formations. The average binding energy (Eb), fragmentation energy (EF), second-order energy difference (Δ2E), adiabatic detachment energy (ADE), and adiabatic electron affinity (AEA) of the CaBn clusters were calculated to investigate the relative stability and the ability of removing or obtaining an electron. As shown by the results, EF and Δ2E values had obvious odd-even alteration as n increased, which indicated that the formations CaB4, CaB6, and CaB8 were more stable. The ADE values for CaBn clusters with even values of n were higher than those with odd values of n, which indicated CaBn clusters with even values of n had difficultly removing an electron. The AEA values of CaB3 and CaB7 were larger than the others, which meant CaB3 and CaB7 easily obtained an electron. These results provide a useful reference for understanding the formation mechanism and stability of the alkaline earth metal boride as well as guidance for synthesizing the CaBn clusters.

Identification and Evaluation of Inhibitors of Lipase from Malassezia restricta using Virtual High-Throughput Screening and Molecular Dynamics Studies

Recent studies revealed the role of lipase in the pathogenicity of Malassezia restricta in dandruff and seborrheic dermatitis (D/SD). The lipase from M. restricta (Mrlip1) is considered a potential target for dandruff therapy. In this work, we performed structure-based virtual screening in Zinc database to find the natural bioactive inhibitors of Mrlip1. We identified three compounds bearing superior affinity and specificity from the Traditional Chinese Medicine database (~60,000 compounds), and their binding patterns with Mrlip1 were analyzed in detail. Additionally, we performed three sets of 100 ns MD simulations of each complex in order to understand the interaction mechanism of Mrlip1 with known inhibitor RHC80267 and the newly identified compounds such as ZINC85530919, ZINC95914464 and ZINC85530320, respectively. These compounds bind to the active site cavity and cause conformational changes in Mrlip1. The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) studies suggested that the average binding energy was stronger in the case of Mrlip1-ZINC85530919 and Mrlip1-ZINC95914464. The selected natural inhibitors might act as promising lead drugs against Mrlip1. Further, the present study will contribute to various steps involved in developing and creating potent drugs for several skin diseases including dandruff.