Computational investigation of impact of Pb(II) and Ni(II) ions on hUNG enzyme: insights from molecular dynamics simulations

Human uracil DNA glycosylase (hUNG), a crucial player in the initiation of the base excision repair pathway, is susceptible to alterations in function and conformation induced by the accumulation of toxic metals. Despite the recognized impact of toxic metals on DNA repair enzymes, there exists a notable deficiency in theoretical investigations addressing this phenomenon. This study investigates the impact of toxic heavy metal ions, Pb(II) and Ni(II), on the stability of hUNG through molecular dynamics (MD) simulations. The initial analysis involved the identification of key cavities in the hUNG enzyme. Notably, the active site cavity emerged as a promising site for ligand binding. Subsequently, AutoDockTools software was employed to dock Pb(II) and Ni(II) onto the identified cavities, followed by extensive MD simulations. The MD analysis, encompassing parameters such as root mean square deviation, radius of gyration, solvent accessible surface area, hydrogen bond variations, Ramachandran plot, principal component analysis, and root mean square fluctuations, collectively revealed distinct alterations in the behavior of the enzyme upon complexation with Pb(II) and Ni(II). Interestingly, the enzyme exhibited enhanced structural stability, reduced flexibility, and modified hydrogen bonding patterns in the presence of these toxic metal ions. The observed limitation in structural flexibility implies a more rigid and stable conformation when the enzyme complex with Pb(II) and Ni(II) compared to its free form. This structural alteration may lead to a potential reduction in enzymatic activity, suggesting that toxic metal ions influence the functional dynamics of hUNG. These computational findings offer valuable insights into the molecular interactions between metal ions and enzymes.Communicated by Ramaswamy H. Sarma.

Fabrication and characterization of a flexible and disposable impedance-type humidity sensor based on polyaniline (PAni)

This work presents a highly sensitive, economical, flexible, and disposable humidity sensor developed with a facile fabrication process. The sensor was fabricated on cellulose paper using polyemaraldine salt, a form of polyaniline (PAni), via the drop coating method. A three-electrode configuration was employed to ensure high accuracy and precision. The PAni film was characterized using various techniques including ultraviolet-visible (UV-vis) absorption spectroscopy, Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD) and scanning electron microscopy (SEM). The humidity sensing properties were evaluated through electrochemical impedance spectroscopy (EIS) in a controlled environment. The sensor exhibits a linear response with R 2 = 0.990 for impedance over a wide range of (0%-97%) relative humidity (RH). Further, it displayed consistent responsiveness, a sensitivity of 1.1701 Ω/%RH, acceptable response (≤220 s)/recovery (≤150 s), excellent repeatability, low hysteresis (≤2.1%) and long-term stability at room temperature. The temperature dependence of the sensing material was also studied. Due to its unique features, cellulose paper was found to be an effective alternative to conventional sensor substrates according to several factors including compatibility with the PAni layer, flexibility and low cost. These unique characteristics make this sensor a promising option for use in specific healthcare monitoring, research activities, and industrial settings as a flexible and disposable humidity measurement tool.

Impact of Cd(II) on the stability of human uracil DNA glycosylase enzyme; an implication of molecular dynamics trajectories on stability analysis

Uracil DNA glycosylase is a key enzyme that identifies and removes damaged bases from DNA in the base excision repair pathway. Experimentalists have identified the possibility of Cd(II) reducing the activity of human uracil DNA glycosylase (hUNG) by binding with the enzyme replacing the catalytic water molecule. The present study focus on the stability variation of the enzyme in the presence and absence of Cd(II) and confirms the reported results with the stability analysis done using molecular dynamic (MD) simulation trajectories. The CavityPlus web server identified seven cavities for the free enzyme as possible binding sites and a cavity containing the active site of the enzyme as the best binding cavity for a ligand. Based on the CavityPlus results and the previously reported work, a free hUNG system and two systems of the enzyme with Cd(II); one with Cd(II) replacing the catalytic water molecule in the active site of the enzyme and the other replacing a non-catalytic water molecule in the active site were generated for the simulation. The simulation trajectories were used for the structural stability analysis of the enzyme in all three systems. The binding free energy of the Cd(II) with the enzyme was calculated using molecular mechanics Poisson Boltzmann surface area method. The results showed that the enzyme achieves comparatively high stability with the removal of catalytic water of the enzyme by Cd(II). Therefore, this supports the previously reported idea that Cd(II) replaces catalytic water molecules and affects enzyme activity.

Cracking a cancer code histone deacetylation in epigenetic: the implication from molecular dynamics simulations on efficacy assessment of histone deacetylase inhibitors

Epigenetic changes, histone acetylation and deacetylation in chromatin have been intensively studied due to their significance in regulating the gene expression. According to the type of tumor, the levels of histone deacetylases (HDAC) are varied. HDAC inhibitors are a new promising class of compounds that inhibit the proliferation of tumor cells. In this study, the inhibitory efficacy of some HDAC inhibitors such as vorinostat, panobinostat, abexinostat, belinostat, resminostat, dacinostat and pracinostat was studied using molecular dynamics simulation. The inhibitory efficacy was estimated by computing the enzyme's stability, positional stability of the individual amino acids and interaction energies of HDLP-inhibitor complexes. It is hoped that this investigation may improve our understanding of the atomic-level description of the inhibitor binding site and how the HDAC inhibitors change the environment of the enzyme's active site. The results obtained from the root-mean-square deviation, the radius of gyration, solvent-accessible surface area, root-mean-square fluctuation, stride server and Ramachandran plot have revealed that the stability of HDLP enzyme with vorinostat, panobinostat and abexinostat is higher than the other studied complexes. According to the calculated values for MM-PBSA, LIE, semi-LIE binding free energies and interaction energies, the stability of the HDLP enzyme varies as panobinostat > abexinostat > vorinostat where resminostat complex showed relatively low stability. The ligandability and drugability values also give the same trend as above. The findings revealed that the panobinostat and abexinostat are potential lead compounds as reference inhibitor vorinostat. Therefore, it is possible to use these drugs as HDAC inhibitors in clinical practices. Also, the outcomes of this study could be utilized to identify new inhibitors for clinical research.Communicated by Ramaswamy H. Sarma.

Polyaniline/palladium nanohybrids for moisture and hydrogen detection

Palladium nanoparticles display fascinating electronic, optical and catalytic properties, thus they can be used for various applications such as sensor fabrication. Conducting polymers such as polyaniline have also been widely used in sensor technology due to its cost effectiveness, versatility, and ease of synthesis. In this research, attention was given to unify the exceptional properties of these two materials and construct palladium nanoparticle coated polyaniline films to detect hydrogen and moisture. Electrochemical polymerization of aniline was carried out on gold sputtered epoxy resin boards. Polyaniline film was generated across a gap of 0.2 mm created by a scratch made on the gold coating prior to electrochemical polymerization. A palladium nanoparticle dispersion was prepared using sonochemical reduction method and coated on to polyaniline film using drop-drying technique. Polyaniline only films were also fabricated for comparative analysis. Sensitivity of films towards humidity and hydrogen was evaluated using impedance spectroscopy in the presence of the respective species. According to the results, polyaniline films exhibited an impedance drop in the presence of humidity and the response was significantly improved once palladium nanoparticles were incorporated. Interestingly, polyaniline only films did not respond to hydrogen. Nevertheless, palladium nanoparticle coated polyaniline films exhibited remarkable response towards hydrogen.

Fluorescence Characteristics of [(Benzoyloxy)methyl]anthracene Donor-Acceptor Systems

A theoretical investigation on fluorescence properties of [(benzoyloxy)methyl]anthracene derivatives containing different groups (OCH3, CH3, H, CF3, F, CN, and NO2) as substituent on the phenyl ring is reported. Electron transfer rate constants for the molecules were calculated using Marcus theory. Theoretical electron transfer rate constants agreed with experimentally observed trend of fluorescence quenching. Large electron transfer rate constants were obtained for molecules containing strongly electron withdrawing groups as the substituent on the phenyl ring. Calculations were conducted at Hartree-Fock and density functional (HF/6-31G(d) and B3LYP/6-31G(d)) levels of theory. Density functional theory predicted spurious charge transfer excited states for molecules containing NO2, CN, and CF3 as the substituent on the phenyl ring.

Contribution of dissolved sulfates and sulfites in hydrogen sulfide emission from stagnant water bodies in Sri Lanka

Accumulation of sulfur-containing compounds and their bacterial mediated reductions have led to the emission of pungent odors from stagnant water bodies. This study is focused on the contribution of inorganic sulfur compounds in the emission of hydrogen sulfide. The measured dissolved oxygen levels have demonstrated good negative correlations with the dissolved sulfide levels implying the oxygen deficiency is the key for the reduction of sulfate ion and sulfite ion to sulfide ion. Particularly, the dissolved molar fractions of sulfide from the total dissolved sulfur compounds (sulfates, sulfites and sulfides) have a very good correlation with the dissolved oxygen for the stagnant water bodies except the artificially aerated prawn farms. For the stagnant water bodies with significant correlations, linear regressions are reported for them to be utilized in estimating one component of the regression from the measurement of the other. The measured data were further utilized to estimate the levels of hydrogen sulfide gas. The pH of the water bodies has confined much of the dissolved sulfides in the form of bisulfide ion and they can be easily escaped to the atmosphere upon acidification due to industrial discharges and/or acidic precipitations. The estimated levels of hydrogen sulfide just above the water surface were plotted for the most polluted stagnant water body in Sri Lanka for the pH range of 5-10 and temperature range of 25-35 degrees C.

Cyclohexane oxidation and carbon deposition over metal oxide catalysts

Catalytic activity of V, Mn, Ni, Cu, Zn, Mo, Zr and Ce oxides over an alpha-alumina support was evaluated for cyclohexane oxidation under oxygen deficient conditions in order to understand the relation between carbon deposition and catalytic activity/selectivity. Carbon formation over the catalysts during the oxidation reaction was measured by means of Fourier transformed infrared spectroscopy (FTIR). Catalysts Mn/Al2O3 and Ce/Al2O3, which are selective for deep oxidation of cyclohexane, possessed relatively carbon free surfaces. The catalysts with relatively high carbon deposition (V, Ni, Cu, Zn, Mo and Zr) produced CO in addition to CO2. Traces of formaldehyde were produced over the catalysts Mo and V.