Synthesis and antimicrobial bioassays of 1,3,4-thiadiazole sulfone derivatives containing amide moiety: A study based on molecular dynamics (MD) simulations,MM/GBSA,and molecular docking

The backbone structure (1,3,4-thiadiazole sulfone derivatives containing amide moiety) of target compounds was determined by modification and optimization of the theoretical design based on commercial chemical carboxin, including molecular docking, scaffold hopping, ligand expansion, etc.In this paper, 23 target compounds were synthesized by the combination of theoretical design and chemical synthesis, and characterized by ¹H NMR, ¹³C NMR and HR MS. Addtionally, the antibacterical bioassay showed that most target compounds performed excellent inhibition on Xanthomonas axonopodis pv. citri (Xac) and Xanthomonas oryzae pv. oryzae (Xoo) in vitro. Meanwhile, molecular docking, molecular dynamics (MD) simulations, and studies on ligand/protein (carboxin/2FBW and 4n/2FBW) complex systems were displayed, and the interaction patterns of ligand/protein complex system were predicted by molecular docking. Besides, the ligand/protein complex system was subject to MD simulation. The analysis of molecular dynamics such as RMSD values suggested that compound/2FBW complexes were stable. MM/GBSA (Molecular mechanics generalized born surface area) dynamic binding affinity results revealed that the active residues (TYR58, HIS26, ARG43, SER39, etc.) played an essential part in the binding of the compound(s) to form a stable low-energy ligand/protein complex, while the MD trajectories demonstrated that the interactions of drugs with 2FBW affected the tertiary structure and increased the stability of protein. Besides, compound 4n also showed control efficacies (curative and protective) on Xoo in vivo, where the curative efficacy was 35.91% and the protective efficacy was 18.97%. In a word, this study showed that 1,3,4-thiadiazole sulfone derivatives containing amide moiety designed based on the structure of carboxin were promising agricultural antibacterial agents, featuring certain stability of binding affinity to proteins and carboxin.     

Shellfish waste-derived mesoporous chitosan for impressive removal of arsenic(V) from aqueous solutions: A combined experimental and computational approach

Novel shellfish waste-derived chitosan (CS) has been developed to adsorb As(V) from simulated wastewater under evaluating adsorption process parameters. The coexistence of some competing ions, like SiO₃^2-, Cl^-, NO₃^– and PO₄^3- as well as the regeneration capacity of the spent adsorbent, was explored. The experimental data were modeled using several kinetics and isotherm models to understand the mechanism related to the uptake process. As(V) uptake was relatively rapid and highly dependent on pH. The Avrami-fractional-order expression supported data best, while the Liu equation described well isotherm data at pH 5.0. The maximum uptake capability (Liu) was 12.32 mg/g, and the highest removal performance (99 %) was obtained at optimum pH 5.0. Molecular dynamics simulations were performed to more clearly illuminate the atomic-level interactions between arsenic species and CS surface in both acidic and basic mediums. After four adsorption–desorption cycles, CS exhibited more than 90 % As(V) removal efficiency. The results of this study indicates that low cost shellfish derived chitosan is promising for efficient removal of As(V) from water body and can be used to remove other pollutants from watewater.     

p‐Toluate‐bridged dinuclear Cu(II) complexes in combination with tridentate chelating ligand: Crystal structure,density functional theory calculation,DNA/protein binding and catecholase activity

The dinuclear Cu(II) complexes [Cu₂(L¹)₂(mb)]?ClO₄ ( 1 ) and [Cu₂(L²)₂(mb)]?ClO₄ ( 2 ) (HL¹ = 2‐[(2‐diethylaminoethylimino)methyl]phenol; HL² = 2‐[1‐(2‐diethylaminoethylimino)propyl]phenol; mb = 4‐methylbenzoate) were synthesized and characterized using X‐ray crystal structure analysis and spectroscopic methods. Complexes 1 and 2 are dinuclear with distorted square pyramidal Cu (II) geometries, where Schiff base coordinates with tridentate (N,N,O) chelating mode and mb bridges two metal centres. Optimized structures and photophysical properties of ligands and complexes were calculated using density functional theory and time‐dependent density functional theory methods using B3LYP functional with 6‐31G (d,p) and LanL2MB basis sets. Interactions of the complexes with bovine serum albumin (BSA) and human serum albumin (HSA) were studied using UV–visible absorption and fluorescence spectroscopies and the calculated values of association constants (M^?1) are 1.7 × 10⁵ ( 1 –BSA), 5.7 × 10⁵ ( 2 –BSA), 1.6 × 10⁵ ( 1 –HSA) and 6.9 × 10⁵ ( 2 –HSA). Interactions of the complexes with calf thymus DNA were also investigated and the binding affinities are 1.4 × 10⁵ and 1.6 × 10⁵ M^?1 for 1 and 2 , respectively. Both complexes catalytically oxidize 3,5‐di‐tert‐butylcatechol to 3,5‐di‐tert‐butylbenzoquinone in the presence of molecular oxygen.     

Discovery of potential inhibitors targeting the kinase domain of polynucleotide kinase/phosphatase (PNKP): Homology modeling,virtual screening based on multiple conformations,and molecular dynamics simulation

In recent years, the level of interest has been increased in developing the DNA-repair inhibitors, to enhance the cytotoxic effects in the treatment of cancers. Polynucleotide kinase/phosphatase (PNKP) is a critical human DNA repair enzyme that repairs DNA strand breaks by catalyzing the restoration of 5’-phosphate and 3’-hydroxyl termini that are required for subsequent processing by DNA ligases and polymerases. PNKP is the only protein that repairs the 3′-hydroxyl group and 5′-phosphate group, which depicts PNKP as a potential therapeutic target. Besides, PNKP is the only DNA-repair enzyme that contains the 5′-kinase activity, therefore, targeting this kinase domain would motivate the development of novel PNKP-specific inhibitors. However, there are neither crystal structures of human PNKP nor the kinase inhibitors reported so far. Thus, in this present study, a sequential molecular docking-based virtual screening with multiple PNKP conformations integrating homology modeling, molecular dynamics simulation, and binding free energy calculation was developed to discover novel PNKP kinase inhibitors, and the top-scored molecule was finally submitted to molecular dynamics simulation to reveal the binding mechanism between the inhibitor and PNKP. Taken together, the current study could provide some guidance for the molecular docking based-virtual screening of novel PNKP kinase inhibitors.     

Electronic and steric effects of substituents on the conformational diversity and hydrogen bonding of N-(4-X-phenyl)-N′,N″-bis(piperidinyl) phosphoric triamides (X = F, Cl, Br, H, CH3): A combined experimental and DFT study

Phosphoric triamides of the general formula (4-X-C₆H₄NH)P(O)(NC₅H₁₀)₂, X = F (1), Cl (2), Br (3), H (4) and CH₃ (5), have been synthesized and characterized. X-ray crystallography at 120 K reveals that the compounds 1, 3, 4·H₂O and 5 are composed of one, four, two and four conformers, respectively. DFT calculations were performed to investigate the electronic structures of the compounds. The X-ray data and DFT calculations revealed that the conformational diversity in these compounds is mainly governed by the steric effects of the substituent X rather than by electronic effects. Although substituent X does not participate directly in hydrogen bonding, the crystal packing of the compounds is influenced by the size of X. Atoms in molecules (AIM) and natural bond orbital (NBO) analyses confirm that the para substituent X has no significant effect on the electronic features of the amidic proton and the phosphoryl oxygen atom (O_P). Using X-ray crystallography, AIM and NBO analyses, the structural and electronic aspects of inter- and intramolecular hydrogen bonds of the compounds have been studied. The charge density (ρ) at the bond critical point (bcp) of the N-H bond decreases from the fully optimized monomers to their corresponding hydrogen bonded clusters. The N-H stretching frequency decreases from the calculated values to the experimental results.     

Synthesis,characterization, density functional theory calculations,and in vitro antibacterial activity of novel transition metal complexes containing an O3-tridentate amoxicillin-based Schiff base: A silver(II) complex as alternative against Pseudomonas aeruginosa resistant to amoxicillin

Transition metal complexes containing an amoxicillin-based Schiff base (H₂L, 3 ) obtained from the condensation of amoxicillin 1 with salicylaldehyde 2 were prepared. Spectroscopic and physicochemical techniques, namely, UV–visible, Fourier-transform infrared spectroscopy, ¹H NMR, electron paramagnetic resonance, transmission electron microscopy, mass spectrometry, magnetic susceptibility, molar conductance, density functional theory (DFT) calculations, together with elemental and thermal analyses were used to characterize the synthesized complexes. Based on these studies, the general formulae [ML(H₂O)₃], where M = Mn 4 , Ni 5 , Zn 6 , and [ML(H₂O)], where M = Cu 7 , Ag 8 , were proposed for the complexes. The amoxicillin-based Schiff base ligand behaved as a dianionic O₃-tridentate chelating agent. DFT studies and magnetic and spectral data revealed octahedral geometries for Mn, Ni, and Zn atoms and distorted tetrahedral geometries for Cu(II) and Ag(II) complexes. Synthesized compounds were tested for antibacterial activity by both agar disk diffusion method and the minimum inhibitory concentration. in vitro bacterial viability revealed that complex 5 had similar antibacterial activity as 1 against Staphylococcus aureus and Staphylococcus epidermidis, whereas Pseudomonas aeruginosa, resistant to amoxicillin, was sensitive to complex 8 . The antibacterial activity of complex 8 could be attributed to its greater catalytic activity as shown by DFT calculations. Toxicity bioassay of the tested compounds showed LC₅₀ values > 1000 ppm, indicating their nontoxicity against brine shrimp nauplii (Artemia salina).     

A novel series of M(II) complexes of 6‐methylpyridine‐2‐carboxylic acid with 4(5)methylimidazole: Synthesis,crystal structures, α‐glucosidase activity,density functional theory calculations and molecular docking

Novel complexes of 6‐methylpyridine‐2‐carboxylic acid and 4(5)methylimidazole, namely [Mn(6‐mpa)₂(4(5)MeI)₂] ( 1 ), [Zn(6‐mpa)₂(4(5)MeI)₂] ( 2 ), [Cd(6‐mpa)₂(4(5)MeI)₂] ( 3 ), [Co(6‐mpa)₂(4(5)MeI)₂] ( 4 ), [Ni(6‐mpa)₂(4(5)MeI)(OAc)] ( 5 ) and [Cu(6‐mpa)₂(4(5)MeI)] ( 6 ), were synthesized for the first time. The structures of complexes 1 – 4 and complexes 5 and 6 were determined using X‐ray diffraction and mass spectrometric techniques, respectively. The experimental spectral analyses for these complexes were performed using Fourier transform infrared and UV–visible techniques. The α‐glucosidase inhibition activity values (IC₅₀) of complexes 1 – 6 were identified in view of genistein reference compound. Moreover, the DFT/HSEh1PBE/6‐311G(d,p)/LanL2DZ level was used to obtain optimal molecular geometry and vibrational wavenumbers for complexes 1 – 6 . Electronic spectral behaviours and major contributions to the electronic transitions were investigated using TD‐DFT/HSEh1PBE/6‐311G(d,p)/LanL2DZ level with conductor‐like polarizable continuum model and SWizard program. Finally, in order to investigate interactions between the synthesized complexes ( 1 – 6 ) and target protein (template structure S. cerevisiae isomaltase), a molecular docking study was carried out.     

Electronic structure and molecular properties of binuclear group VII pentalene metal carbonyl complexes [C8H6{M(CO3)}2] (M = Mn,Tc, Re,Bh): A relativistic density functional theory study

Homobimetallic systems where the metals are linked through a pentalenediide ligand, of the type anti-[Pn{M(CO)₃}₂] (Pn = pentalenediide), which include transition metals of the group VII with M = ₂₅Mn (1), ₄₃Tc (2), ₇₃Re (3) and ₁₀₇Bh (4), and the syn-[Pn{M(CO)₃}₂] isomer with M = ₂₅Mn (s1), ₄₃Tc (s2), ₇₃Re (s3) and ₁₀₇Bh (s4), were studied with relativistic all-electron density functional (DFT) calculations, including spin-orbit (SO) coupling via the two components ZORA Hamiltonian. The electronic structure was studied in detail in the four systems. Broken symmetry calculations were performed for all the paramagnetic systems to verify their mixed-valence character. The infrared (IR) spectra were obtained at the scalar relativistic regime and the UV–Vis was obtained by time-dependent spin-orbit DFT and compared against the experimental data available (only for 1 and 3). The relative binding energy calculations predict that the not yet reported s1, 2, s2, 4 and s4 complexes may be synthesized. Their optical and vibrational properties are described here.