No abstract

Drug discovery and the process of new drug design have been formulated much easier in the past two decades by introducing, proliferation of combined physical, biochemical process from computing capabilities and computational approaches. Since the breast cancer is one of the life-threatening problems globally, no effective prescription is still now invented or not available in the market or medical treatment. Although the few number of drugs is just touched on the market, the remedy has consisted of severe side effects and low efficiency. Regarding that fact, the D-glucofuranose and its derivatives have been designed by the quantum calculation, molecular docking, ADMET and SAR analysis. For molecular docking, the cancer protease (3hb5) and triple-negative breast cancer protease (4pv5) are selected for study whereas the binding affinity of cancer protease (3hb5) is found at ranging from -6.20 to -10.40 kcal/mol, and it is slightly lower than triple-negative breast cancer protease (4pv5). Next, the molecular dynamic has performed to make the validation of docking complex. In our forthcoming study, it has shown that the 03, 05, and 08 compounds could be considered the potential drug comparison with standard drug. These three drugs completed all the criteria, including high binding energy, non-toxic, non-carcinogenic, and highly soluble in biological system.

The α-D-glucopyranoside and its derivatives were as the cardinal investigation for developing an effective medication to treat the highest deadly white spot syndrome virus (WSSV) diseases in Shrimp. In our forthcoming work, both computational tools, such as molecular docking, quantum calculations, pharmaceutical kinetics, ADMET, and their molecular dynamics, as well as the experimental trial against WSSV, were executed to develop novel inhibitors. In the beginning, molecular docking was carried out to determine inhibitors of the four targeted proteins of WSSV (PDB ID: 2ED6, 2GJ2, 2GJI, and 2EDM), and to determine the binding energies and interactions of ligands and proteins after docking. The range of binding affinity was found to be between −5.40 and −7.00 kcal/mol for the protein 2DEM, from −5.10 to 6.90 kcal/mol for the protein 2GJ2, from −4.70 to −6.2 kcal/mol against 2GJI, and from −5.5 kcal/mol to −6.6 kcal/mol for the evolved protein 2ED6 whereas the L01 and L03 display the highest binding energy in the protein 2EDM. After that, the top-ranked compounds (L01, L02, L03, L04, and L05), based on their high binding energies, were tested for molecular dynamics (MD) simulations of 100 ns to verify the docking validation and stability of the docked complex by calculating the root mean square deviation (RMSD) and root mean square fluctuation (RMSF). The molecules with the highest binding energy were then picked and compared to the standard drugs that were been applied to fish experimentally to evaluate the treatment at various doses. Consequently, approximately 40–45% cure rate was obtained by applying the dose of oxytetracycline (OTC) 50% with vitamin C with the 10.0 g/kg feed for 10 days. These drugs (L09 to L12) have also been executed for molecular docking to compare with α-D-glucopyranoside and its derivatives (L01 to L08). Next, the evaluation of pharmacokinetic parameters, such as drug-likeness and Lipinski’s principles; absorption; distribution; metabolism; excretion; and toxicity (ADMET) factors, were employed gradually to further evaluate their suitability as inhibitors. It was discovered that all ligands (L01 to L12) were devoid of hepatotoxicity, and the AMES toxicity excluded L05. Additionally, all of the compounds convey a significant aqueous solubility and cannot permeate the blood-brain barrier. Moreover, quantum calculations based on density functional theory (DFT) provide the most solid evidence and testimony regarding their chemical stability, chemical reactivity, biological relevance, reactive nature and specific part of reactivity. The computational and virtual screenings for in silico study reveals that these chosen compounds (L01 to L08) have conducted the inhibitory effect to convey as a possible medication against the WSSV than existing drugs (L09, L10, L11 and L12) in the market. Next the drugs (L09, L10, L11 and L12) have been used in trials.

No abstract

Natural organic pigments such as carotenoids, betalains, anthocyanins, and carminic acid are notably found as safer food preservatives compared to other harmful synthetic chemicals. Due to glycosylation and acylation, betalains exhibit a broad-spectrum antimicrobial functionality with protection against degenerative diseases. Thus, betalains have been investigated as a potential bacterial inhibitor for food preservative applications. Initially, 36 betalain derivatives have been taken for primary screening using molecular docking. Afterward, the top ten ligands are taken for further study and analysis. The results of Prediction of Activity Spectrum of Substances (PASS) assured the antibacterial capabilities of betalains, and Lipinski's rule-of-five ensures the acceptability of the selected ligands as antibacterial inhibitors. The bacterial pathogens, such as C. botulinum (3FIE), E. coli (2ZWK), and S. typhi (3UU2) are selected for molecular docking by these betalain pigments. Furthermore, ADMET investigations and QSAR studies are performed to check insights into the bacterial inhibition process. Most active and common binding sides were observed at GLY159, ASN165, and SER166 for C. botulinum, at ASP8, LYS40, and TRP50 for E. coli; and at ARG37, GLN5, and ARG74 for S. typhi. The present study clearly shows an excellent insight towards the invention of plant-based new organic inhibitors to face the challenges of bacterial-resistant common food preservatives.

No abstract

For developing the stannite type quarterly crystal photocatalyst, the electronic structure and optical properties of ZnAg 2 GeSe 4 , ZnAg 2 Ge 0.93 Fe 0.07 Se 4 and ZnAg 2 Ge 0.86 Fe 0.14 Se 4 were calculated and compared with the parent stannite type quarterly crystal, ZnAg 2 GeS 4 . First of all, the four functionals, such as GGA with PBE, GGA with RPBE, GGA with WC and LDA with CA-PZ functionals were used for primary screening of electronic band structure and structural geometry for ZnAg 2 GeS 4 while the band gap was in 0.93, 0.97, 0.77 and 0.67 eV, respectively. It must be mentioned that the experimental value of ZnAg 2 GeS 4 was 0.94 eV so that the GGA with PBE showed the overlapping value of band gap. The main focus of this paper is to evaluate the band structure of newly predicted the stannite type quarterly crystal, ZnAg 2 GeSe 4 using four methods replacing the Sulfur atom by Serium atom on ZnAg 2 GeS 4 . The band gap for four methods, such as GGA with PBE, GGA with RPBE, GGA with WC and LDA with CA-PZ functionals, were calculated in 0.84 eV, 0.92 eV, 0.68 eV and 0.58 eV. Afterward, Fe atom was doped by two portions, like 7% and 14%, to make the empirical formula, ZnAg 2 Ge 0.93 Fe 0.07 Se 4 and ZnAg 2 Ge 0.86 Fe 0.14 Se 4 . The numerical values of band gaps for ZnAg 2 Ge 0.93 Fe 0.07 Se 4 and ZnAg 2 Ge 0.86 Fe 0.14 Se 4 were 0.43 eV, 0.53 eV, 0.35 eV and 0.18 eV and 0.24 eV, 0.31 eV, 0.18 eV and 0.08 eV, respectively, using the four respected DFT methods. For their contributed orbitals of each atom on crystal, the density of state and the partial density of state for ZnAg 2 GeSe 4 , ZnAg 2 Ge 0.93 Fe 0.07 Se 4 and ZnAg 2 Ge 0.86 Fe 0.14 Se 4 crystals were simulated through the GGA with PBE method as standard regarding the calculation of band gap study comparison with experimental magnitude. For giving the further information about the nature in case of optical evidence, the six optical properties, such as absorption, reflection, refractive index, conductivity, dielectric function and loss function were calculated, and make a comparative study. In case of UV light absorption in lighten to optical parameters, the ZnAg 2 Ge 0.86 Fe 0.14 Se 4 can show the highest absorption up to convenience energy region as photocatalyst.

Electronic band structures, the total density of state, partial density of state and optical properties were investigated using first principle method for Ag2BiO3 via Generalized Gradient Approximation (GGA) based on the Perdew-Burke-Ernzerhof (PBE0). The band gap was found to be 0.490 eV which is supported for good semiconductor. The density of state and partial density of state were simulated for evaluating the nature of 5s, 4d for Ag, 6s, 4f, 5d, 6p for Bi and 2s, 2p for oxygen atom for Ag2BiO3 orbital travelling from the maximum valance band to minimum conduction band to explain the transition of electron due to hybridization. The optical properties including, absorption, reflection, refractive index, conductivity, dielectric function and loss function were calculated which can account for the superior absorption of the visible light. The key point of this research study was to determine the activity on electronics structure and optical properties for Fe doped by 12%. Regarding the band gap and optical properties, Ag2Bi0.88Fe0.12O3 can give more conductivity compared with that than of the Ag2BiO3, showing as a superconductor. Electronic structure Band gap Density of states Optical properties