This work presents a molecular level investigation on the nature and mode of binding between imidazolium-based ionic liquids (ILs) ([Cnbim]Br where n = 2, 4, 6) with calf thymus DNA. This investigation offers valuable insight into the mechanisms of interactions that can affect the structural features of DNA and possibly cause the alteration or inhibition of DNA function. To expedite analysis, the study resorted to using molecular docking and COnductor like Screening MOdel for Real Solvents (COSMO-RS) in conjunction with fluorescence spectroscopic data for confirmation and validation of computational results. Both the fluorescence and docking studies consistently revealed a weak interaction between the two molecules, which corresponded to the binding energy of a stable docking conformation in the range of −5.19 to −7.75 kcal mol−1. As predicted, the rod-like structure of imidazolium-based ILs prefers to bind to the double-helix DNA through a minor groove. Interestingly, the occurrence of T-shape π-π stacking was observed between the amine group in adenine that faces the aromatic ring of imidazole. In addition, data of COSMO-RS for the interaction of individual nucleic acid bases to imidazolium-based ILs affirmed that ILs showed a propensity to bind to different bases, the highest being guanine followed by cytosine, thymine, uracil, and adenine.
An acid, 2,2-dichloropropionic acid (2,2-DCP) is an active ingredient in herbicide (Dalapon®). Using 2,2-DCP as a model substrate, an alkalotolerant bacterium was successfully isolated from the Blue Lake, Turkey. This bacterium is a potential bioremediation agent of recalcitrant xenobiotic halogenated compounds. This study aimed to prove the efficacy of the alkalotolerance Bacillus megaterium BHS1 in degrading 2,2-DCP as the sole source of carbon. Biolog GEN III system and 16S rRNA analysis were used for the identification of the bacterium. It was discovered that the strain BHS1 is Bacillus megaterium, and the bacterium that was observed to thrive in alkaline conditions (pH 7.0−14.0), supplemented with varying concentrations of 2,2-DCP (from 20 to 60 mM). Growth of strain BHS1 was exceptional in 40 mM of 2,2-DCP at pH 9, corresponding to a cell doubling time of 17.7 hour, whereas was fully inhibited at 50 mM 2,2-DCP. Since halogenated pollutants can make their way into highly alkaline environments, therefore, identifying threshold levels of strain BHS1 with respect to alkaline-tolerance and maximum level of 2,2-DCP may prove pertinent. This is to ensure that an optimal environment is created for the bacteria to degrade 2,2-DCP-contaminated water. In addition, this is the first study exploring a Bacillus species isolated from an alkaline environment adept in utilizing 2,2-DCP as a sole source of carbon. Hence, the ability of this strain to degrade other types of haloalkanoic acids constitutes a worthy future study.
Newbouldia laevis, also known as the African Border Tree or Fever Tree, is a deciduous tree native to West Africa. The plant is valued for its medicinal properties and is used in traditional medicine for its antimicrobial and anti-inflammatory effects. N. laevis, is a storage tank of phytochemicals with huge health benefits and performances globally for the treatment and management of numerous disease conditions. Limited research exists on the usage of N. laevis for hepatocellular carcinoma (HCC) treatment. This study aims to explore the inhibitory activities of phytochemicals from N. laevis against the hexokinase 2 protein, a target in hepatocarcinoma (HCC) treatment. This study presents a unique in silico approach that includes ligand binding site prediction, molecular docking, molecular dynamics simulation, and Molecular Mechanics Poisson–Boltzmann Surface Area (MM/PBSA) methods. A total of 35 phytochemicals with available 3D structures were identified through literature mining. The literature review highlighted the significance of hexokinase 2 protein as a target inhibitor in the treatment of hepatocellular carcinoma (HCC). Molecular docking experiment with the all the identified phytochemicals and hexokinase 2 revealed that all the identified phytochemicals had potential inhibitory activities against the target protein. Moreover, chrysarobin, apigenin and ursolic acid were the best inhibitors with lowest binding energy of −8.9 kcal/mol, −8.7 kcal/mol, and −8.5 kcal/mol, respectively. The docking experiment was validated by comparing the binding affinities with known reference drug Cabozantinib-S-malate (−8.3 kcal/mol). Further, molecular dynamics studies of complexes with the best docking scores and reference drug complexes were described in detail here. The results of 100 ns modeling (RMSD, RMSF, Rg and SASA) show extraordinary stability during the establishment of complexes with apigenin and ursolic acid, as well as favorable binding energy, which was determined theoretically by means of the MM/PBSA method, thereby increase the probability of their acting as promising and likely hexokinase 2 inhibitors. Therefore, the study predicted that apigenin and ursolic acid could be used as a potential inhibitor/antagonist for the hexokinase 2 enzyme.
Polyethylene terephthalate (PET) pollution is an emerging environmental hazard because of its recalcitrance to degradation. This study proposes an in silico mutagenesis of LipKV1 from Acinetobacter haemolyticus for improved lipase-PET interaction, using the PET-degrading Thermobifida cutinase (TfCut2) as the structural benchmark. Results revealed that lid deletion on LipKV1 (LipKV1_LE) facilitated the entry of PET into the active site. The mutation of several predicted amino acids into alanine expanded the LipKV1 active site for better PET binding. Docking results indicated that the LipKV1_LE mutants, Var9 (-6.2 kcal/mol), Var18 (-6.0 kcal/mol), and Var181 (-6.0 kcal/mol), produced higher binding affinities with PET than the wild-type LipKV1 (-2.5 kcal/mol) and TfCut2 (-4.6 kcal/mol), attesting that the selected mutation sites played prominent role in altering the abilities of LipKV1_LE mutants to bind to PET. Our molecular dynamics (MD) simulation results corroborated the variant-PET complexes' improved binding, mirrored by their improved conformations (RMSD ∼0.35 nm). The RMSF results also showed acceptable fluctuation limits of the LipKV1_PET mutant complexes (RMSF < 0.5 nm). Rg data of the complexes showed that they are conformationally stable, with a maximum of three H-bonds in their interaction with PET. SASA results showed that the mutations did not profoundly alter the hydrophobicity of the amino acid residues. MM-PBSA calculations on the LipKV1_PET mutant complexes estimated binding free energies between −28.29 kcal/mol to −23.25 kcal/mol, comparable to the molecular docking data. Thus, the MD data conveyed the practicality of the above-said site mutations in rationally designing the LipKV1 active site for better PET degradation.
Molecular recognition, particularly enantiomeric specificity of biological molecules is a key consideration in designing drugs, pharmaceutical intermediate and in industrial production of chirally active intermediate. Although the molecular bases of many enzymes stereospecificity are not completely delineated, a number of protein engineering studies were able to enhance and even in some cases invert the stereospecificity of various enzymes. Herein, we review the current understanding on enzymes stereospecificity, and the effects of mutations to the stereospecific pockets due to enzymes engineering to improve stereospecificity.
Abstract The present study aimed to investigate the decolorization of various commercial dyes through bioinformatics analysis, utilizing techniques such as molecular docking, molecular dynamics simulation, and Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA). These analyses were conducted on different commercial dyes to evaluate their potential for biodegradation. In this study, four commercial dyes, namely acid orange 7, cresol red, methylene blue, and malachite green, were selected as potential targets for degradation by azoreductases (AzrBmH21, AzrBmH22/3, and AzrBmH24/5) derived from Bacillus megaterium H2. The prediction of ligand binding or catalytic sites for AzrBmH21, AzrBmH22/3, and AzrBmH24/5 was performed using a machine learning algorithm based on the Prank Web and DeepSite chemoinformatic tool. The analysis revealed that several amino acids of AzrBmH2 interacted with the tested dyes, indicating the presence of distinct ligand-binding sites for AzrBmH2-dye complexes. The binding affinity for AzrBmH21, AzrBmH22/3, and AzrBmH24/5 ranged from − 9.4 to -5.5 kcal/mol, -9.2 to -5.4 kcal/mol, and − 9.0 to -5.4 kcal/mol, respectively. Each complex was stabilized by a minimum of 0–5 hydrogen bonds. MD simulations revealed stable AzrBmH2-dye complexes (with RMSD 0.15–0.42 nm, RMSF 0.05–0.48 nm, Rg 1.75–1.88 nm). MMPBSA calculations indicated that the AzrBmH2-dye complexes, except for AzrBmH2-malachite green, exhibited the lowest binding energy (-191.05 ± 7.08 to 314.19 ± 6.88 kcal/mol). The AzrBmH2-malachite green complex showed a prevalence of hydrophobic interactions (-268.25 ± 12.25 to -418.92 ± 29.45 kcal/mol) through van der Waals forces. This study highlights the potential role of enzymes, specifically azoreductases from Bacillus megaterium H2, in predicting the decolorization of commercial dyes. These findings contribute to our understanding of enzyme mechanisms in bioremediation and for biotechnological applications.
Consumption of iced beverages is common in Malaysia although specific research focusing on its safety parameters such as presence of faecal coliforms and heavy metal elements remains scarce. A study conducted in Kelantan indicated that faecal coliforms were detected in the majority of the ice cube samples analyzed, largely attributable to improper handling. Hence, it was found pertinent to conduct similar study in other parts of the country such as Johor Bahru if the similar pattern prevailed. Therefore, this present cross sectional study which randomly sampled ice cubes from 30 permanent food outlets in Taman Universiti, Johor Bahru for detecting contamination by faecal coliforms and selected heavy metal elements (lead, copper, manganese and zinc) acquires significance. Faecal coliforms were detected in 11 (36.67%) of the samples, ranging between 1 CFU/100 mL to > 50 CFU/100 mL; two of the samples were grossly contaminated (>50 CFU/100 mL). Interestingly, while positive detection of lead was observed in 29 of the 30 ice cube samples (mean: 0.511±0.105 ppm; range: 0.489-0.674 ppm), copper, manganese and zinc were not detected. In addition, analysis on commercially bottled mineral water as well as in tap water samples did not detect such contaminations. Therefore, it appears that (1) contamination of faecal coliforms in ice cubes in food outlets in Malaysia may not be sporadic in pattern but rather prevalent and (2) the source of water used for manufacturing the ice cubes that contained significant amount of lead would suggest that (3) it was neither originated from the treated tap water supply nor bottled mineral water or (4) perhaps contaminated during manufacturing process. Further studies exploring the source of water used for manufacturing these ice cubes as well as the handling process among food operators deserve consideration.
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