DFT study on the effect of proximal residues on the Mycobacterium tuberculosis catalase-peroxidase (katG) heme compound I intermediate and its bonding interaction with isoniazid

Biodegradation of environmental pollutants using catalase-based biocatalytic systems

The synergistic combination of biocatalysts and nanomaterials provides a new interface of a robust biocatalytic system that can effectively remediate environmental pollutants. Enzymes, such as catalase-based constructs, impart the desired candidature for catalytic transformation processes and are potential alternatives to replace conventional remediation strategies that have become laborious and somewhat inefficient. Furthermore, the controlled or uncontrolled discharge of various emerging pollutants (EPs) into water bodies is equally proportional to the fast-growing population and extensive urbanization. EPs affect the entire living being and continuously deteriorate the environmental system, directly or indirectly. The occurrence of EPs (even released after partial treatments, but still in bioactive forms) disturbs ecological integrity. Due to the ineffectiveness of in-practice traditional remediation processes, new and robust treatment measures as effective and sustainable remediation have become a meaningful goal. In this context, special attention has been shifted to engineering an enzyme (catalase)-based biodegradation system with immense prospects in environmental cleanup. The unique synergistic combination of nanomaterials (having multifunctional attributes) with enzymes of interest makes them a state-of-the-art interface that can further ameliorate bio-catalysis and biodegradation performance. This review covers current research and scientific advancement in developing and deploying catalase-based biocatalytic systems to mitigate several EPs from the environment matrices. The biocatalytic features of catalase, along with the mechanistic insight into H₂O₂ neutralization, several nano-based materials loaded with catalase, including nanoparticles (NPs), carbon nanotubes (CNTs), metal-organic frameworks (MOFs), polymeric-based composites, oxime-functionalized cryo-gel disks, electro-spun nanofibrous membranes, and other hybrid materials have also been discussed with suitable examples.

α-Helix in Cystathionine β-Synthase Enzyme Acts as an Electron Reservoir

The modulation of electron density at the Pyridoxal 5'-phosphate (PLP) catalytic center, because of charge transfer across the α-helix/PLP interface, is the determining factor for the enzymatic activities in the human Cystathionine β-Synthase (hCBS) enzyme. Applying density functional theory calculations, in conjunction with the real space density analysis, we investigated the charge density delocalization across the entire heme-α-helix-PLP electron communication channels. The electron delocalization due to hydrogen bonds at the heme/α-helix and α-helix/PLP interfaces are found to be extended over a very long range, as a result of redistribution of electron densities of the cofactors. Moreover, the internal hydrogen bonds of α-helix that are crucial for its secondary structure also participate in the electron redistribution through the structured hydrogen-bond network. α-Helix is found to accumulate the electron density at the ground state from both of the cofactors and behaves as an electron reservoir for catalytic reaction at the electrophilic center of PLP.

Mechanistic insights into the chemistry of compound I formation in heme peroxidases: quantum chemical investigations of cytochrome c peroxidase

Peroxidases are heme containing enzymes that catalyze peroxide-dependant oxidation of a variety of substrates through forming key ferryl intermediates, compounds I and II. Cytochrome c peroxidase (Ccp1) has served for decades as a chemical model toward understanding the chemical biology of this heme family of enzymes. It is known to feature a distinctive electronic behaviour for its compound I despite significant structural similarity to other peroxidases. A water-assisted mechanism has been proposed over a dry one for the formation of compound I in similar peroxidases. To better identify the viability of these mechanisms, we employed quantum chemistry calculations for the heme pocket of Ccp1 in three different spin states. We provided comparative energetic and structural results for the six possible pathways that suggest the preference of the dry mechanism energetically and structurally. The doublet state is found to be the most preferable spin state for the mechanism to proceed and for the formation of the Cpd I ferryl-intermediate irrespective of the considered dielectric constant used to represent the solvent environment. The nature of the spin state has negligible effects on the calculated structures but great impact on the energetics. Our analysis was also expanded to explain the major contribution of key residues to the peroxidase activity of Ccp1 through exploring the mechanism at various in silico generated Ccp1 variants. Overall, we provide valuable findings toward solving the current ambiguity of the exact mechanism in Ccp1, which could be applied to peroxidases with similar heme pockets.

Discerning the feasibility of a no-water peroxidase mechanism in the doublet spin state irrespective of the environment surrounding the heme pocket.

One-Pot Synthesis and in Silico Molecular Docking Studies of Arylselanyl Hydrazides as Potential Antituberculosis Agents

The present study reports a simple two-step method for the synthesis of arylselanyl hydrazide derivatives using hypophosphorous acid and polyethylene glycol (H₃ PO₂ /PEG-400) as an alternative reducing system and hydrazine hydrate (NH₂ NH₂ ⋅xH₂ O/50-60 %). This single-vessel procedure was employed with methyl acrylate 2a and methyl bromoacetate 2b using diaryl diselenides to generate the nucleophile species to produce, respectively, 3-(arylselanyl)propane-hydrazides 4a-e and 2-(arylselanyl)acetohydrazides 5a-e with good yields by accelerating the reduction of -Se-Se- bond, when compared to available methods. The synthesized molecules are structurally similar to the isoniazid (INH). Therefore, we perform in silico molecular docking studies, using the lactoperoxidase enzyme, in order to verify whether the INH Se derivatives could interact in a similar way to INH at the active site of the mammalian enzyme. The in silico results indicated a similar type of interaction of the arylselanyl hydrazide derivatives with that of INH. In view of the similar in silico interaction of the selenium derivatives of INH, the arylselanyl hydrazide derivatives reported here should be tested against Mycobacterium tuberculosis in vitro.