Bio-inspired or biomimetic chemistry deals with the replication of the nature’s fundamental processes, which can help in understanding the functioning of biological systems and develop novel applications. Although a large number of researchers worked towards the replication of natural synthetic pathways through biogenetic syntheses, enzyme mimicry by the small organic molecules and inorganic complexes emerged in leaps and bounds over the years. The development of biomimetic chemistry then continued in designing the molecules that can function like enzymes. And now, with the advent of nanotechnology, nanostructured materials have been shown to exhibit enzyme-like activities (nanozymes). Interestingly, the two distinct fields, biology and materials science, have been integrated to form an entirely new area of research that has captured a great attention. Along with the pronounced application of nanomaterials as drug delivery vehicles, anticancer agents, antimicrobials, etc., research is also focused on designing nanomaterials for the biomimetic applications. The thesis consists of five chapters. The first chapter provides a general overview of the recently discovered nanozymes that mimic heme-peroxidase, oxidase, superoxide dismutase, catalase, haloperoxidase and phosphatase. This chapter also deals with the nanozymes’ application in sensing and immunoassay, and as antioxidants, neuroprotective agents. The factors affecting the nanozymes’ activity and the challenges associated with them is also covered in this chapter. Chapter 2 is divided into two parts and it deals with the biomimetic properties of graphene-based materials. In part A, the remarkable peroxynitrite (PN) reductase and isomerase activities of hemin-functionalized reduced graphene oxide (rGO) is discussed. In part B, the activity of graphene oxide (GO) as peroxide substrate for the glutathione peroxidase (GPx) enzyme is discussed. In chapter 3, the oxidant material, V2O5, is shown to exhibit significant GPx-like antioxidant activity in its nano-form. Chapter 4 deals with the oxidase-like activity of MnFe2O4 nanooctahedrons for the antibody-free detection of major oxidative stress biomarker, carbonylated proteins. In chapter 5, the phosphotriesterase mimetic role of vacancy engineered nanoceria is discussed. instead of H2O2 for glutathione peroxidase (GPx) enzyme. As partial reduction of GO was observed when treated with GPx enzyme due to the fact that large sheet-like structures cannot be accessible to the active site, we studied the reaction with some GPx mimetics (Fig. 2). Varying the concentration of cofactor glutathione (GSH) required for the reaction, GPx mimic, ditelluride, could accomplish the reduction of GO following Michaelis-Menten kinetics. As the structure of GO is elusive and under active investigation, our study highlights the presence of peroxide linkages as integral part of GO other than hydroxyl, epoxy and carboxylic groups. This study also highlights an important fact that the modification of GO by biologically relevant compounds such as redox proteins must be taken into account when using GO for biomedical applications because such modifications can alter the fundamental properties of GO. Figure 2. The GO reductase and decarboxylase activities of GPx mimetic ditelluride compound, suggesting the presence of peroxide linkages on GO. In chapter 3, we have discussed about the novel antioxidant nanozyme that combats oxidative stress. During our attempts in the investigation of antioxidant nanozymes, we surprisingly noticed that the oxidant material, V2O5, shows significant GPx-like antioxidant activity in its nano-form. The Vn readily internalize in the cells and exhibit remarkable protective effects when challenged against reactive oxygen species (ROS). Although Vn has been shown to protect cells from ROS-induced damage, cells treated with bulk V2O5 and few vanadium complexes resulted in generation of ROS and severe toxicity. Detailed investigation on the mechanism of this interesting phenomenon Chapter 4 deals with the development of novel methodology for detection of biomarkers. Inspired by the use of antibodies and enzymes for detection of a specific antigen, we have shown for the first time that the nanozymes can entirely replace antibodies and enzymes in Enzyme-linked Immunosorbent Assays (ELISA). As a specific example, we focused on the antibody-free detection of chief oxidative stress biomarker, carbonylated proteins, as our target. To achieve this, we designed MnFe2O4 nanooctahedrons that can function as oxidase enzyme and form signaling point of detection. We functionalized MnFe2O4 nanooctahedrons with hydrazide terminating groups so that carbonylated proteins can be linked to nanozymes by hydrazone linkage (Fig. 4a). Treatment of various carbonylated proteins (hemoglobin (Hb), Myoglobin (Mb), Cytochrome c (Cyt c), RNase and BSA) coated in well plate with hydrazide-terminated MnFe2O4 nanooctahedrons and then with 3,3’,5,5’-tetramethylbenzidine substrate, resulted in instantaneous detection by well plate reader (Fig. 4b). Considering the challenges and difficulties associated with the conventional methods used to detect such modified proteins, this methodology opens up a new avenue for the simple, cost-effective, instantaneous and entirely antibody-free ELISA-type detection of carbonylated proteins. Our results provide a cumulative application of nanozymes’ technology in oxidative stress associated areas and pave a new way for direct early detection of post translational modification (PTM) related diseases. Figure 4. a) Nanozyme linked to the carbonylated protein coated on a plate through hydrazone linkage. b) General bar diagram showing detection of oxidized (carbonylated) proteins by nanozymes. Synopsis Figure 5. a) A cartoon view of surface of ceria showing vacancy. b) Zoomed portion of high resolution transmission electron microscopic image showing few vacancies on the surface of nanoceria. c) Catalytic mechanism of detoxification of paraoxon at the defect site. In the final chapter, chapter 5, we have discussed about the nanomaterial that can function as phosphotriesterase enzyme. Phosphotriesterase enzyme is a bacterial enzyme that is involved in the rapid hydrolysis of sarin gas-related deadly nerve agents such as paraoxon, parathion and malathion. When encountered with these orgnaophospatetriesters, living beings tend to undergo nerve shock to cause paralysis by inhibiting an extremely important enzyme called acetylcholine esterase. They are also known to cause severe oxidative stress problems and are associated with neurodegenerative disorders. Therefore, curbing the toxic effects and detoxification of these nerve agents is a world-wide concern and many research teams have focused their attention to address this important problem. Working on the development of nanozymes for important problems, we found that nanoceria, especially the vacancy engineered one (Fig. 5a,b), can serve as active mimic of phosphotriesterase enzyme in the presence of N-methylmorpholine (acting as a distal base histidine). Vacancy engineered nanoceria has been shown to catalyze the hydrolysis of high amounts of paraoxon quiet efficiently and within few minutes with very low activation energy and high kcat. Detailed mechanistic investigation revealed that the presence of both Ce(III) and Ce(IV) is very essential for detoxification activity (Fig. 5b). The vacancies on the surface of nanoceria, were the buried Ce(III) ions are directly exposed to the reaction environment, behave as hotspots or enzyme active sites for detoxification reaction (Fig. 5b).

The role of mitochondria is multidimensional and ranges in vast areas, including apoptosis, cellular response towards stress, metabolism, which is regulated by a plethora of proteins, acting together to maintain cellular and organellar homeostasis. In spite of the presence of mitochondrial DNA, most of the mitochondrial proteins are nuclear encoded and translocated inside the organelle through dedicated translocases present on outer and inner membrane of mitochondria. To fulfil the cellular energy demand, mitochondria efficiently generate ATP by oxidative phosphorylation, and thus are considered as "power house of cell." There occurs a transfer of electrons from various oxidizable substrates to oxygen, which is achieved by a series of redox reactions with generation of water as a byproduct. This process is coupled with ATP synthesis, involves five protein-complexes present in the inner mitochondrial membrane. During this process, it generates extremely reactive intermediate species of oxygen as a byproduct collectively referred as Reactive Oxygen Species (ROS) through partial reduction of oxygen. These intermediate metabolites of oxygen include superoxide anion (O2-º), H2O2 and highly reactive hydroxyl radicals (OHº). Although ROS are produced by different cellular sources, such as widely expressed and evolutionary conserved NADPH Oxidases, xanthine oxidase, cyclooxygenases, lipoxygenases and cytochrome P450 enzymes but mitochondria are one of the major contributors of cellular ROS. Earlier, reactive oxygen species were considered as harmful but for past few decades, the role ROS has been appreciated as signalling molecules. Because of their high reactivity, these species can cause redox mediated modifications to cellular components and thus have an ability to participate in signalling process. The regulation of signalling pathway by ROS is governed by either alterations in cellular redox conditions or by oxidative modifications of certain residues in proteins, which are involved in signalling cascades. Reactive Oxygen Species can modify amino acid residues, interact with Fe-S clusters or other metal complexes and induce dimerization of proteins to alter protein structure and function. ROS causes modifications to critical amino acids, mainly by oxidation of cysteine residues, where oxidation of sulfhydryl group (-SH) of a single cysteine residue leads to formation of sulfenic (-SOH), sulfinic (-SO2H), sulfonic (-SO3H), or S-glutathionylated (-SSG) derivatives. Thus, by incorporating these modifications, ROS affects the function of proteins, thereby modulating the cellular signalling process. On the other hand, the accumulation of higher level of reactive oxygen species may damage cellular components causing oxidative stress. Therefore, it is necessary to maintain the ROS levels and regulation of intracellular redox homeostasis depends upon a complex network of antioxidant molecules. These antioxidants range from low molecular weight glutathione to large proteins like glutathione peroxidases. Cell has an array of antioxidants with different subcellular locations. Superoxide Dismutase which catalyzes dismutation of superoxides and converts them to H2O2, localizes in cytosol, mitochondrial intermembrane space and extracellular matrix. Different isoforms of Glutatione Peroxidases (GPx) and Peroxiredoxins (Prx) are located in cytosol as well as in mitochondria and scavenge H2O2 by using glutathione (GSH) and thioredoxin (Trx) respectively, as co-factors. During this peroxidase activity of GPx and Prx, GSH and Trx get oxidized and recycled back to the reduced form by Glutathione Reductase (GR) and Thioredoxin Reductase (TR) correspondingly, with the help of NADPH. Thus, GPx system (GPx, GR, GSH and NADPH) and Prx system (Prx, Trx, TR and NADPH) helps in maintenance of redox balance by scavenging H2O2. Catalase is present in peroxisomes for the catalytic degradation of H2O2. Along with Thioredoxin, glutaredoxin (Grx) also reduces protein disulphides and maintains the redox homeostasis. Although, reactive oxygen species are important for normal physiological process, oxidative stress caused by imbalanced ROS levels is thought to be involved in progression of many disorders. However, in most of the diseases, the role of ROS is not yet clear. Elevated oxidative stress is observed with insulin resistance and progression of type II diabetes mellitus, and the resultant high glucose levels alter mitochondrial physiology, leading to the fragmentation of organelle. However, on contrary it has also been observed that ROS improves insulin sensitivity. ROS is directly involved in progression of neurodegenerative disorders, which are characterized by oxidative stress mediated neuronal loss. Interestingly, in case of cancer ROS plays a differential role. At moderately higher levels, ROS helps cancer cells to detach from the matrix and thus assist in metastasis but the higher accumulation of ROS leads to oxidative stress mediated cell death. Thus, cancer cells have an enhanced expression level of antioxidants to maintain the optimum ROS concentration for their survival and proliferation. The role of ROS in cellular signalling and progression of diseases highlights the importance of redox regulation. Mitochondria being the major source of ROS, harbours various redox regulators such as a mitochondrial permeability transition pore (mPTP), inner membrane anion channel (IMAC), Ca++ ions, etc. In addition, certain proteins like Hsp31/DJ1 class also translocate into the organelle in a stress dependent manner to maintain redox homeostasis. These proteins are encoded by the nuclear genome and translocated in the organelle, suggesting the importance of mitochondrial import machinery in regulation of redox balance. Another such example is MIA pathway of protein import, where MIA40 regulates ROS indirectly by catalyzing folding of disulfide containing proteins such as SOD-1 in a redox coupled process. However, under most cases, the physiological disorders lead to uncontrolled production of reactive oxygen species, thereby overloading the cellular antioxidant defence machinery. The failure of the antioxidant machinery leads to enhanced disease progression. Under such disease conditions where the upheaval of redox homeostasis leads to the accumulation of ROS, artificial antioxidants can be used to protect cells against oxidative damage. Artificial systems such as Cyclodextrins, metal complexes, porphyrins, polymers, supramolecules and biomolecules such as nucleic acids, catalytic antibodies and proteins, have been created to mimic the structures and functions of natural enzymes through various approaches. In the present thesis, we have elucidated the role of two mitochondrial proteins, which are part of mitochondrial import motor, as redox regulators and the effect of artificial antioxidants in maintenance of redox homeostasis under stress. A detailed description on importance of ROS in cellular signalling and disease progression has been included in Chapter I, which gives a preface for the work mentioned in this thesis. Chapter II to chapter V elucidates the main objectives of the present thesis, which are: 1. Identification of novel human mitochondrial regulators of redox homeostasis • Role of NEF in redox sensing (Chapter II) • Evolved function of J-like protein in ROS regulation (Chapter III) 2. Characterization of potential artificial antioxidants as redox therapeutics • Organo-selenium compounds as potential artificial antioxidants (Chapter IV) • Use of nanoparticles as a natural antioxidant mimics (Chapter V) Chapter II: Mitochondrial Hsp70 (mtHsp70) plays a critical role for the import of the precursor proteins. The import activity of mtHsp70 is attributed by cyclic binding and release of precursor proteins which in turn is regulated by co-chaperones J-proteins and nucleotide exchange factor (NEF). The affinity for substrate is governed by the binding of ADP or ATP at the N-terminal nucleotide binding pocket of mtHsp70. The affinity for substrate is higher in ADP bound state as compared to ATP bound state. mtHsp70 by its ATPase activity hydrolyze ATP (low-affinity state) to ADP (high-affinity state), which is replaced back to ATP by NEF thus maintaining the mtHsp70 cycle for protein import. In the present study, we have biochemically and functionally characterized GrpEL1 and GrpEL2 as a nucleotide exchange factor for mtHsp70. We observed that like their yeast ortholog Mge1, both the mammalian NEFs interacts with mtHsp70 and exchange ADP from ATP to maintain the cycle of mtHsp70. Interestingly, we observed that both the NEFs are part of human mitochondrial import motor and are recruited at the import motor as hetero-subcomplex. The formation of GrpEL1-EL2 hetero-subcomplex is important to maintain the stability of both the NEFs. In this study, we have elucidated that the interplay between the two NEFs governs organellar response towards oxidative stress. Chapter III: Redox imbalance generates multiple cellular damages leading to oxidative stress mediated pathological conditions such as neurodegenerative diseases, diabetes, ageing and cancer progression. Therefore, maintenance of ROS homeostasis is most important, that involves well-defined antioxidant machinery. In the present chapter, we have identified for first time a component of mammalian protein translocation machinery, Magmas, to perform a critical ROS regulatory function. Magmas overexpression has been reported in highly metabolically active tissues, cancer cells and tissues of developmental origin that are prone to oxidative damage. We found that Magmas regulates cellular ROS levels by controlling its production as well as scavenging. Magmas promotes cellular tolerance towards oxidative stress by enhancing antioxidant enzyme activity, thus preventing induction of apoptosis and damage to cellular components. Magmas enhances the activity of ETC-complexes, causing reduced ROS production. Our results suggest that J-like domain of Magmas is essential for maintenance of redox balance. The function of Magmas as an ROS sensor was found to be independent of its role in protein import, underlying its dual role in human mitochondria. The unique ROS modulatory role of Magmas is highlighted by its ability to increase cellular tolerance to oxidative stress even in yeast model organism. The cyto-protective capability of Magmas against oxidative damage makes it an important candidate for future investigation in therapeutics of oxidative stress related diseases. Chapter IV: The dysregulation of antioxidant machinery in oxidative stress mediated disorders lead to accumulation of excess ROS, highlighting the importance of artificial antioxidants. For the therapeutics of oxidative stress related disorders, artificial antioxidants have been used as combination redox therapy. In order to realize potent biocompatible antioxidants with minimum toxicity, we have utilized two approaches – synthesis of organic compounds and nanoparticle based enzyme mimetics. We have synthesized novel isoselenazoles with high glutathione peroxidase (GPx) and peroxiredoxin (Prx) activities, which provide remarkable cytoprotection to human cells, mainly by exhibiting antioxidant activities in the presence of cellular thiols. The cytotoxicity of the isoselenazoles is found to be significantly lower than that of ebselen, which is being widely clinically evaluated by several research groups for the treatment of reperfusion injuries and stroke, hearing loss, and bipolar disorder. The compounds reported in this study has the potential to be used as therapeutic agents for disorders mediated by reactive oxygen species.. Chapter V: Nanomaterials with enzyme-like properties have attracted significant interest, although limited information is available on their biological activities in cells. Here, we show that V2O5 nanowires (Vn) functionally mimic the antioxidant enzyme, glutathione peroxidase by using cellular glutathione as a co-factor. Although a bulk V2O5 is known to be toxic to the cells, the property is altered when converted into a nanomaterial form. The Vn nanozymes readily internalize into mammalian cells of multiple origins (kidney, neuronal, prostate, cervical) and exhibit robust enzyme-like activity by scavenging the reactive oxygen species, when challenged against intrinsic and extrinsic oxidative stress. The Vn nanozymes fully restore the redox balance without perturbing the cellular antioxidant defense, thus providing an important cytoprotection for biomolecules against harmful oxidative damage. Based on our findings, we envision that biocompatible Vn nanowires can provide future therapeutic potential to prevent ageing, cardiac disorders and several neurological conditions, including Parkinson’s and Alzheimer’s disease.

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Die Phospholipid-Hydroperoxid Glutathion-Peroxidase (phGPx) ist ein monomeres Selenoprotein, welches innerhalb der Familie der Glutathion-Peroxidasen aufgrund seiner breiten Substratspezifität und der Fähigkeit Proteinthiole zu modifizieren eine Sonderstellung einnimmt. Vom Gen der phGPx werden nach heutigem Kenntnisstand drei verschiedene Protein-Isoformen gebildet. Die mitochondriale Isoform enthält am N-Terminus ein mitochondriales Insertionssignal und wird bevorzugt im Testis exprimiert. Von einem im Leserahmen stromabwärts liegenden Startkodon wird die kürzere, ubiquitär exprimierte zytosolische Isoform synthetisiert. Eine dritte phGPx-Isoform besitzt eine N-terminale nukleäre Lokalisationssequenz (kodiert von einem alternativen Exon 1) und wird vornehmlich in den Kernen post-meiotischer Zellen der Spermatogenese gefunden. Aufgabe dieser Arbeit war es, die molekularen Mechanismen zu untersuchen, die am Zustandekommen des vielfältigen Expressionsmusters der phGPx-Isoformen beteiligt sind. Im ersten Teil der Arbeit wurden transkriptionelle Regulationsmechanismen der phGPx-Expression untersucht. Im proximalen Promotorbereich (-100 bp – +228 bp) des phGPx-Gens wurden unter in vitro (Supershift-Assay) und in vivo (Chromatin-Immunopräzipitation) Bedingungen die Transkriptionsfaktoren Sp1 und NF-Y identifiziert, die an drei GC-reiche Motive beziehungsweise zwei inverse CCAAT-Boxen binden. Darüber hinaus konnten in kompetetiven Gelshift-Assays im proximalen Promotorbereich zwei Bindungssequenzen identifiziert werden, die von Faktoren der Smad-Familie gebunden werden. Funktionelle in vitro Promotorstudien mit mutierten Promotorkonstrukten zeigten, dass die Mutagenesen der Sp1- und NF-Y Bindestellen einen starken Einfluss auf die Reportergenaktivität hatten. Im zweiten Teil der Arbeit wurden durch Untersuchungen von Protein-RNA-Interaktionen post-transkriptionelle Mechanismen der Expressionsregulation studiert. Mit Hilfe des in vivo Ansatzes des Hefe Drei-Hybrid Systems wurde der Guanin-reiche Sequenz bindende Faktor 1 (GRSF1) identifiziert, der in der 5’-untranslatierte Region der mitochondrialen phGPx-mRNA bindet. In RNA Gelshift-Assays wurde die Spezifität dieser Interaktion bestätigt und näher charakterisiert. Schließlich wurden für GRSF1 und die phGPx Expressionsprofile in murinen Gewebe erstellt sowie die zeitabhängige Expression beider Proteine während der Embryogenese verfolgt. Die auffällig ähnlichen Expressionsmuster lassen ähnliche Regulationsmechanismen vermuten. Die in dieser Arbeit identifizierten trans-regulatorischen Proteine Sp1, NF-Y, Smad und GRSF1 sollten an der differentiellen Expression der phGPx-Isoformen beteiligt sein. / The Phospholipid Hydroperoxide Glutathione Peroxidase (phGPx) is a monomeric selenoprotein that is unique in the family of Glutathione Peroxidases due to its low substrate specificity and its ability to oxidise protein thiols. Three different isoforms are known to derive from one common gene. The mitochondrial Isoform contains an N-terminal mitochondrial insertion sequence and is preferentially expressed in postpubertal testis. The shorter, ubiquitously expressed, cytosolic isoform is expressed from an in-frame start codon. A third isoform contains an N-terminal nuclear localization signal coded for by an alternative exon 1 and is preferentially expressed in the nuclei of post-meiotic spermatides. The aim of the present study is to investigate the molecular mechanisms leading to the different isoforms and causing their tissue specific expression pattern. In the first part of this work transcriptional regulatory mechanisms will be analysed. Within the proximal promoter region (-100 to +228 bp) of the phGPx gene the transcription factors SP1 and NF-Y were identified to bind to three GC-boxes and two CCAAT-boxes respectively using in vitro methods (Supershift Assays) and in vivo methods (Chromatine immunoprecipitation). Moreover, performing competitive gel shift assays two binding elements for the smad family of transcription factors could be identified. Functional in vitro reporter gene assays provided evidence that the mutagenesis of the binding sequences for NF-Y and Sp1 has a strong impact on promoter activity. In the second part of this work post-transcriptional events in the expression regulation of the phGPx were analysed on the basis of protein/RNA interactions. Applying the in vivo approach of the yeast three hybrid system the Guanin-riche sequence binding factor 1 (GRSF1) could be identified binding to the 5’-untranslated region of the mitochondrial phGPx messenger. RNA mobility shift assays were performed to further characterize the specificity of this protein/RNA interaction. Eventually, the tissue distribution of GRSF1 and phGPx was studied in murine tissues and their expression kinetics were followed during murine embryogenesis. The obvious parallel expression kinetics for mitochondrial phGPx and GRSF1 suggest common regulatory mechanisms for these two genes. All the identified trans-regulatory elements are very likely to be involved in the differential expression regulation of the phGPx isoforms.

Background & Aims: Oxidative stress and apoptosis are proposed mechanisms of cellular injury in studies of xenobiotic hepatotoxicity. The aim of this work is to find early signal markers of drug-induced injury of the liver by focusing on select antioxidant/oxidant and apoptotic genes. As well, to address the relationship between conventional liver dysfunction markers and the measured mRNA and protein expressions in the D-galactosamine/lipopolysaccharide and tert-butylhydroperoxide hepatotoxicity models. Furthermore, potential hepatoprotective capabilities of antioxidant polyphenols quercetin and curcumin were evaluated in relation to its modulation of the oxidative stress and apoptotic parameters in the given xenobiotic hepatotoxicity models. Methods: Biochemical markers testing the hepatic function included aminotransferases (ALT, AST) and bilirubin. Measurements of TBARS and conjugated dienes were used to assess lipoperoxidation. Plasma levels of catalase and reduced glutathione were used as indicators of the oxidative status of the cell. Real time PCR was used to analyse the mRNA expressions of the inducible nitric oxide synthase (NOS-2), heme oxygenase-1 (HO-1), superoxide dismutase (SOD-1), glutathione peroxidase (Gpx-1), caspase 3 (Casp3), BH3 interacting domain death agonist (Bid) and Bcl-2...

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