The S-S bridge mutation between the A2 and A4 loops (T416C-I432C) of Cel7A of Aspergillus fumigatus enhances catalytic activity and thermostability.

Disulfide bonds are important for maintaining the structural conformation and stability of the protein. The introduction of the disulfide bond is a promising strategy to increase the thermostability of the protein. In this report, cysteine residues are introduced to form disulfide bonds in the Glycoside Hydrolase family GH 7 cellobiohydrolase (GH7 CBHs) or Cel7A of Aspergillus fumigatus. Disulfide by Design 2.0 (DbD2), an online tool is used for the detection of the mutation sites. Mutations are created (D276C-G279C; DSB1, D322C-G327C; DSB2, T416C-I432C; DSB3, G460C-S465C; DSB4) inside and outside of the peripheral loops but, not in the catalytic region. The introduction of cysteine in the A2 and A4 loop of DSB3 mutant showed higher thermostability (70% activity at 70°C), higher substrate affinity (Km = 0.081 mM) and higher catalytic activity (Kcat = 9.75 min-1; Kcat/Km = 120.37 mM min-1) compared to wild-type AfCel7A (50% activity at 70°C; Km = 0.128 mM; Kcat = 4.833 min-1; Kcat/Km = 37.75 mM min-1). The other three mutants with high B factor showed loss of thermostability and catalytic activity. Molecular dynamic simulations revealed that the mutation T416C-I432C makes the tunnel wider (DSB3: 13.6 Å; Wt: 5.3 Å) at the product exit site, giving flexibility in the entrance region or mobility of the substrate in the exit region. It may facilitate substrate entry into the catalytic tunnel and release the product faster than the wild type, whereas in other mutants, the tunnel is not prominent (DSB4), the exit is lost (DSB1), and the ligand binding site is absent (DSB2). This is the first report of the gain of function of both thermostability and enzyme activity of cellobiohydrolase Cel7A by disulfide bond engineering in the loop.IMPORTANCEBioethanol is one of the cleanest renewable energy and alternatives to fossil fuels. Cost efficient bioethanol production can be achieved through simultaneous saccharification and co-fermentation that needs active polysaccharide degrading enzymes. Cellulase enzyme complex is a crucial enzyme for second-generation bioethanol production from lignocellulosic biomass. Cellobiohydrolase (Cel7A) is an important member of this complex. In this work, we engineered (disulfide bond engineering) the Cel7A to increase its thermostability and catalytic activity which is required for its industrial application.

Optimized structure of monoubiquitinated FANCD2 (human) at Lys 561: a theoretical approach.

Fanconi anaemia pathway repairs inter-strand cross linking damage (ICL) of the DNA. Monoubiquitination of FANCD2 and FANCI is very crucial for ICL repairing. In this work we have tried to understand the monoubiquitinated FANCD2 structure, which facilitates the FANCD2 for binding the damage part of the chromatin. Crystal structure of the monoubiquitinated FANCD2 alone is not available, therefore we have modelled the optimized structure of the human monoubiquitinated (Lys 561) FANCD2. As there is no suitable software or web server we have developed a method for building up monoubiquitinated product and validated on simplest monoubiquitinated protein, diubiquitin. We have predicted the structure of human monoubiquitinated FANCD2 by using our method and studied the interaction with DNA by docking studies. Molecular Dynamics (MD) simulation has been used to understand the stability of the structure. Large structural differences have been observed between FANCD2 and monoubiquitinated FANCD2. Docking studies with DNA suggest that the binding site varies for the FANCD2 and monoubiquitinated FANCD2.Communicated by Ramaswamy H. Sarma.

Antibacterial activities of sulfamethoxazolyl-azo-phenols and their Cu(II) complexes along with molecular docking properties.

Sulfamethoxazolyl-azo-phenols [SMX-N=N-C6H2(R)(R/)-OH] (1a, 2a) and their Cu(II) complexes, [Cu(SMX-N=N-C6H2(R)(R/)-O)2] (1b, 2b) (R = p-OMe, R/ = H, 1a/1b; R = p-Cl, R/ = m-CH3, 2a/2b) show antibacterial sensitivity against Gram-positive bacteria, B. subtillis; IC50: 281.47 ± 1.84 µM (1a), 126.39 ± 1.66 µM (1b), and 279.94 ± 3.15 µM (2a), 123.62 ± 1.27 µM(2b), and Gram-negative bacteria, E. coli; IC50: 204.66 ± 3.31 µM (1a) and 89.05 ± 1.48 µM (1b), 223.13 ± 2.71 µM (2a), and 98.26 ± 1.59 µM (2b). Interaction of DNA with free ligand (1a and 2a) is insignificant, while the complexes (1b and 2b) interact strongly and the binding constants are K b, 8.413 × 104 M-1 (1b) and 6.56 × 105 M-1 (2b). Optimized structures of the compounds are docked with protein structure of DHPS (E. coli) to propose the most favoured binding mode of the drugs in the active site. The in silico test of the compound helps to understand drug metabolism, drug-protein interactions, and toxicity (ADMET).

Structural characterization of new Schiff bases of sulfamethoxazole and sulfathiazole, their antibacterial activity and docking computation with DHPS protein structure.

New Schiff bases (1, 2) of substituted salicylaldehydes and sulfamethoxazole (SMX)/sulfathiazole (STZ) are synthesized and characterized by elemental analysis and spectroscopic data. Single crystal X-ray structure of one of the compounds (E)-4-((3,5-dichloro-2-hydroxybenzylidene)amino)-N-(5-methylisoxazol-3-yl)benzenesulfonamide (1c) has been determined. Antimicrobial activities of the Schiff bases and parent sulfonamides (SMX, STZ) have been examined against several Gram-positive and Gram-negative bacteria and sulfonamide resistant pathogens; the lowest MIC is observed for (E)-4-((3,5-dichloro-2-hydroxybenzylidene)amino)-N-(thiazol-2-yl)benzene sulfonamide (2c) (8.0 µg mL(-1)) and (E)-4-((3,5-dichloro-2-hydroxybenzylidene)amino)-N-(5-methylisoxazol-3-yl)benzene sulfonamide (1c) (16.0 µg mL(-1)) against sulfonamide resistant pathogens. DFT optimized structures of the Schiff bases have been used to carry out molecular docking studies with DHPS (dihydropteroate synthase) protein structure (downloaded from Protein Data Bank) using Discovery Studio 3.5 to find the most preferred binding mode of the ligand inside the protein cavity. The theoretical data have been well correlated with the experimental results. Cell viability assay and ADMET studies predict that 1c and 2c have good drug like characters.

The spectroscopic characterization, photochromism of cadmium(II)-iodo complexes of 1-alkyl-2-(arylazo)imidazoles and DFT computation of representative complexes.

[Cd(Raai-C(n)H(2n+1))(µ-I)I]2 and [Cd(Raai-C(n)H(2n+1))2I2] are synthesized by the reaction of CdI2 with 1-alkyl-2-(arylazo)imidazole (Raai-C(n)H(2n+1), n=4, 6, 8) in MeOH in 1:1 and 1:2 M ratio of salt and ligands, respectively. The complexes have been characterized by spectral data (UV-Vis, IR, (1)H NMR, Mass). The coordinated Raai-C(n)H(2n+1) shows photochromism, E(trans)-to-Z(cis) isomerisation, upon UV light irradiation. The reverse process, Z-to-E, is very slow in visible light irradiation process while the reaction is sensitive to change of reaction temperature. The quantum yields (ϕE→Z) for E-to-Z and the activation energy (Ea) of Z-to-E isomerisation are calculated and found that the complexes show subordinate results compared to free ligand. DFT computations of two representative complexes were carried out to explain the spectral and photochromic phenomena.

The crystal structure of sulfamethoxazole, interaction with DNA, DFT calculation, and molecular docking studies.

Sulfamethoxazole (SMX) [4-amino-N-(5-methyl-1,2-oxazol-3-yl)benzenesulfonamide] is structurally established by single crystal X-ray diffraction measurement. The crystal packing shows H-bonded 2D polymer through N(7)-H(7A)-O(2), N(7)-H(7B)-O(3), N(1)-H(1)-N(2), C(5)-H(5)-O(3)-S(1) and N(7)-(H7A)-O(2)-S(1). Density Functional Theory (DFT) and Time Dependent-DFT (TD-DFT) computations of optimized structure of SMX determine the electronic structure and has explained the electronic spectral transitions. The interaction of SMX with CT-DNA has been studied by absorption spectroscopy and the binding constant (Kb) is 4.37×10(4)M(-1). The in silico test of SMX with DHPS from Escherichia coli and Streptococcus pneumoniae helps to understand drug metabolism and accounts the drug-molecule interactions. The molecular docking of SMX-DNA also helps to predict the interaction feature.

A novel 2,6-diformyl-4-methylphenol based chemosensor for Zn(II) ions by ratiometric displacement of Cd(II) ions and its application for cell imaging on human melanoma cancer cells.

A new chelating ligand [4-methyl-2,6-bis-(pyridin-2-yl-hydrazonomethyl)-phenol] (1) was prepared by the condensation of 2-hydrazinylpyridine with 2,6-diformyl-p-cresol. Compound 1 exhibits weak fluorescence due to intramolecular photoinduced electron transfer (PET). The sensor (1) demonstrates Zn(2+)-specific emission enhancement due to the "PET off" process through a 1:1 binding mode with the metal ion. The fluorescence quantum yield of chemosensor 1 is only 0.020, and it increases more than 14-fold (0.280) in the presence of one equivalent of the zinc ion. Interestingly, the introduction of other metal ions causes the fluorescence intensity to remain either unchanged or weakened except for Cd(2+). The new sensor showed 'naked-eye' detection of Zn(2+) ions: a color change of the solution from colorless to yellow. Ratiometric displacement of Cd(2+) ions from the complex by Zn(2+) ions supports the formation of a more stable sensor­Zn(2+) complex over the sensor­Cd(2+) complex. The experimental findings have been correlated with theoretical results using the B3LYP functional and 6-31G (d, p), LANL2DZ basis set for Cd(2+) (2) and Zn(2+) (3) complexes, respectively, by the Density Functional Theory (DFT) method. Moreover, the ability of probe 1 to sense Zn(2+) within human melanoma cancer cells has been explored, and the Zn(2+)-probing process in living cells was found to be reversible with zinc chelator solution of N,N,N,N-tetrakis(2-pyridylmethyl)ethylenediamine (TPEN) or EDTA.