In silico prediction of 3D structure of Mn superoxide dismutase of Scylla serrata and its binding properties with inhibitors

Annonaceous acetogenins as promising DNA methylation inhibitors to prevent and treat leukemogenesis - an in silico approach

Leukemia is a haematological malignancy affecting blood and bone marrow, ranking 10th among the other common cancers. DNA methylation is an epigenetic dysregulation that plays a critical role in leukemogenesis. DNA methyltransferases (DNMTs) such as DNMT1, DNMT3A and DNMT3B are the key enzymes catalysing DNA methylation. Inhibition of DNMT1 with secondary metabolites from medicinal plants helps reverse DNA methylation. The present study focuses on inhibiting DNMT1 protein (PDB ID: 3PTA) with annonaceous acetogenins through in-silico studies. The docking and molecular dynamic (MD) simulation study was carried out using Schrödinger Maestro and Desmond, respectively. These compounds' drug likeliness, ADMET properties and bioactivity scores were analysed. About 76 different acetogenins were chosen for this study, among which 17 showed the highest binding energy in the range of -8.312 to -10.266 kcal/mol. The compounds with the highest negative binding energy were found to be annohexocin (-10.266 kcal/mol), isoannonacinone (-10.209 kcal/mol) and annonacin (-9.839 kcal/mol). MD simulation results reveal that annonacin remains stable throughout the simulation time of 100 ns and also binds to the catalytic domain of DNMT1 protein. From the above results, it can be concluded that annonacin has the potential to inhibit the DNA methylation process and prevent leukemogenesis.Communicated by Ramaswamy H. Sarma.

Molecular interaction mechanisms and cellular response of superoxide dismutase and catalase to fluoranthene

As an important raw material and intermediate product of the petrochemical industry, fluoranthene (Fla) can be emitted with industrial activities and has become a typical polycyclic aromatic hydrocarbon enriched in the Chinese topsoil layer, posing a significant threat to sensitive soil biota. Here, multispectral tools and molecular simulation techniques were integrated to elucidate the molecular mechanism of Fla interaction with key antioxidant enzymes superoxide dismutase (SOD) and catalase (CAT) at the molecular level. Meanwhile, we further revealed the cellular responses of SOD and CAT and the associated redox states in earthworm (Eisenia fetida) coelomocytes based on the molecular-level results. Our results showed that the exposure to Fla affected the backbone structure of SOD and CAT molecules and resulted in the formation of Fla-SOD polymers as well as an overall reduction in the size of the Fla-CAT binding system. Fla altered the microenvironment around Tyr residues in the SOD molecule and quenched the endogenous fluorescence of Tyr within the CAT molecule. In earthworm coelomocytes, Fla at 60 and 80 μM resulted in a significant elevation of CAT and SOD activities by 114% (p = 0.032) and 6.09% (p = 0.013), respectively. Molecular simulation results suggested that Fla-induced changes in the structure and conformation of SOD and CAT may be the key reason for their altered activities. The related redox homeostasis detection in earthworm coelomocytes indicated that high concentrations (80 μM) of Fla led to a significant accumulation of intracellular ROS (p = 0.018) and resulted in the development of lipid peroxidation. Our work contributes to an in-depth understanding of the biological effect of Fla to sensitive soil fauna, thus providing new ideas for Fla ecological risk prevention and control.

Spatio-temporal changes in oxidative stress physiology parameters in apple snail Pila globosa as a function of soil Mg, Ca, organic carbon and aquatic physico-chemical factors

Information on the oxidative stress physiology parameters (OSPP) in general and as a function of the fluctuation of Mg, Ca and organic carbon present in soil and aquatic physico-chemical factors such as pH, temperature and salinity in particular are scanty in the amphibious snail Pila globosa. A spatio-temporal analysis of redox metabolism (as OSPP) followed by discriminant function analysis of the obtained data were performed in P. globosa sampled from the east-coasts of Odisha state, India (mostly along the Bay of Bengal) for environmental health assessment purposes. Results revealed that the OSPP are susceptible to seasonal synergistic variation of soil and physico-chemical factors. Overall, lipid peroxidation, total antioxidant capacity, activities of catalase, glutathione reductase had positive correlation whereas ascorbic acid, the reduced glutathione and the activity of superoxide dismutase had non-significant correlation with the soil Mg, Ca, organic carbon, and pH, temperature and salinity of water. In the summer season, the snails had a marked 51.83% and 26.41% higher lipid peroxidation level and total antioxidative activity as compared to the other seasons. Spatial variation of OSPP indicates that snails residing away from the Bay of Bengal coast had at least 4.4% lower antioxidant level in winter and 30% higher lipid peroxide levels in summer as compared to the rest of the sampling sites. Results on OSPP in P. globosa may be useful for monitoring the ecotoxic effects of environment using molluscs in general and P. globosa in particular.

Nurture to nature via COVID-19, a self-regenerating environmental strategy of environment in global context

Coronavirus Disease (COVID-19) has become the largest pandemic that has affected 210 countries. Rolling data indicate that 257,3605 people are infected by the disease, from which 701,838 have recovered and 178,562 have died. No specific medicine or vaccine is available yet to control the disease, hence, social distancing via lockdown is widely adopted as the only preventive measure. Social distancing is observed at different level of strictness in different counties but it almost made the world to stands still. Although scientific articles on this largest social move are scanty, it resulted in benefiting the deteriorated environment to revive back. Many environmental indices such as lowering NO₂ and CO₂ emissions and reduction in particulate matters in air as a result of less human activities have led to clean air and pollution free water in many countries. Undoubtedly, the world was experiencing pollution in several countries due to mainly human activities including urbanization, industrialization, fossil fuel exhaustion etc. Under such situation a special (natural) a protective measure was awaited to fix environmental issues. Probably, the lockdown is one of the natural effects expected by nature via introduction of COVID-19. It is because, introduction of COVID-19 to nature was an outcome of mutation from two of its pre-existing forms, although, debate on it is still continuing. Viability of CoV-19 virus found to have a lot of correlation with aquatic and terrestrial environmental parameters such as pH, surface type, temperature etc. Air pollution is found to increase the risk of COVID-19 infection, therefore, use of mask and alcohols based standard sterilisers is strongly recommended. However, the self-revival rate of nature shall continue during post-lockdown period and a master plan must be adapted by national and international (mostly political) bodies to revive the Mother Nature completely.

Inter nation social lockdown versus medical care against COVID-19, a mild environmental insight with special reference to India

Infection by coronavirus (CoV-19) has led to emergence of a pandemic called as Coronavirus Disease (COVID-19) that has so far affected about 210 countries. The dynamic data indicate that the pandemic by CoV-19 so far has infected 2,403,963 individuals, and among these 624,698 have recovered while, it has been fatal for 165,229. Without much experience, currently, the medicines that are clinically being evaluated for COVID-19 include chloroquine, hydroxychloroquine, azithromycin, tocilizumab, lopinavir, ritonavir, tocilizumab and corticosteroids. Therefore, countries such as Italy, USA, Spain and France with the most advanced health care system are partially successful to control CoV-19 infection. India being the 2nd largest populous country, where, the healthcare system is underdeveloped, major portion of population follow unhygienic lifestyle, is able to restrict the rate of both infection and death of its citizens from COVID-19. India has followed an early and a very strict social distancing by lockdown and has issued advisory to clean hands regularly by soap and/or by alcohol based sterilizers. Rolling data on the global index of the CoV infection is 13,306, and the index of some countries such as USA (66,148), Italy (175,055), Spain (210,126), France (83,363) and Switzerland (262,122) is high. The index of India has remained very low (161) so far, mainly due to early implementation of social lockdown, social distancing, and sanitizing hands. However, articles on social lockdown as a preventive measure against COVID-19 in PubMed are scanty. It has been observed that social lockdown has also drastic impacts on the environment especially on reduction of NO2 and CO2 emission. Slow infection rate under strict social distancing will offer time to researchers to come up with exact medicines/vaccines against CoV-19. Therefore, it is concluded that stringent social distancing via lockdown is highly important to control COVID-19 and also to contribute for self-regeneration of nature.

Possible activation of NRF2 by Vitamin E/Curcumin against altered thyroid hormone induced oxidative stress via NFĸB/AKT/mTOR/KEAP1 signalling in rat heart

Oxidative stress is implicated in both hypo- and hyper-thyroid conditions. In the present study an attempt has been made to elucidate possible interaction between vitamin E or/and curcumin (two established antioxidants) with active portion (redox signaling intervening region) of nuclear factor erythroid 2-related factor 2 (NRF2) as a mechanism to alleviate oxidative stress in rat heart under altered thyroid states. Fifty Wistar strain rats were divided into two clusters (Cluster A: hypothyroidism; Cluster B: hyperthyroidism). The hypo- (0.05% (w/v) propylthiouracil in drinking water) and hyper- (0.0012% (w/v) T4 in drinking water) thyroid rats in both clusters were supplemented orally with antioxidants (vitamin E or/and curcumin) for 30 days. Interactive least count difference and principal component analyses indicated increase in lipid peroxidation, reduced glutathione level, alteration in the activities and protein expression of antioxidant enzymes like superoxide dismutase, catalase, glutathione peroxidase and glutathione reductase under altered thyroid states. However, the expression of stress survival molecules; nuclear factor κB (NFκB) and the serine-threonine kinase B (Akt), in hyper-thyroidism only points towards different mechanisms responsible for either condition. Co-administration of vitamin E and curcumin showed better result in attenuating expression of mammalian target for rapamycin (mTOR), restoration of total protein content and biological activity of Ca²⁺ ATPase in hyperthyroid rats, whereas, their individual treatment showed partial restoration. Since NRF2 is responsible for activation of antioxidant response element and subsequent expression of antioxidant enzymes, possible interactions of both vitamin E or/and curcumin with the antioxidant enzymes, NRF2 and its regulator Kelch ECH associating protein (KEAP1) were studied in silico. For the first time, a modeled active portion of the zipped protein NRF2 indicated its interaction with both vitamin E and curcumin. Further, curcumin and vitamin E complex showed in silico interaction with KEAP1. Reduction of oxidative stress by curcumin and/or vitamin E may be due to modulation of NRF2 and KEAP1 function in rat heart under altered thyroid states.

Transport Stress Changes Blood Biochemistry, Antioxidant Defense System, and Hepatic HSPs mRNA Expressions of Channel Catfish Ictalurus punctatus

Transport procedures usually cause fish stress. The purpose of this study was to investigate the effect of transport stress on blood biochemical profiles, oxidative stress biomarkers, and hepatic heat shock proteins (HSPs) of channel catfish (Ictalurus punctatus). Fish (body weight 55.57 ± 5.13 g) were randomly distributed to two groups, the control, and the treatment. The control group was kept under the normal culture conditions. The treatment group was exposed to the process of transport (3.5 h). Fish samples were collected before transport, after packing and at 0, 1, 6, 24, 72, and 168 h after transport, respectively. Transport caused a significant increase in the serum concentrations of cortisol, glucose, total cholesterol, and triglyceride, as well as, the activity of aspartate aminotransferase at 0 and 1 h after transport compared with non-transported fish and the basal level. Blood total protein content significantly declined in the transported fish. Total antioxidant capacity (T-AOC), malonaldehyde content, and the activities of both glutathione peroxidase and catalase significantly increased in fish within 6 h after transport. The transported fish exhibited a significant higher level in either the concentration of nitric oxide or the mRNA expressions of both hepatic HSP70 and HSP90. It is concluded that transport triggers stress response of I. punctatus, leading to the obvious change in antioxidant capacity. I. punctatus need to be more care after transport to recover from transport stress.

Activity of antioxidant enzymes in response to atmospheric pressure induced physiological stress in deep-sea hydrothermal vent mussel Bathymodiolus azoricus

Deep sea hydrothermal Bathymodiolus azoricus mussels from Portuguese EEZ Menez Gwen hydrothermal field possess the remarkable ability to overcome decompression and survive successfully at atmospheric pressure conditions. We investigated the potential use of antioxidant defense enzymes in mussel B. azoricus as biomarkers of oxidative stress induced by long term acclimatization to atmospheric pressure conditions. Mussels collected at Menez Gwen hydrothermal field were acclimatized for two weeks in three distinct conditions suitable of promoting physiological stress, (i) in plain seawater for concomitant endosymbiont bacteria loss, (ii) in plain seawater under metal iron exposure, (iii) constant bubbling methane and pumped sulfide for endosymbiont bacteria survival. The enzymatic activities of superoxide dismutase (SOD), catalase (CAT), and iron storage proteins in addition to electrophoretic profiles were examined in vent mussel gills and digestive gland. Gills showed approximately 3 times more SOD specific activity than digestive glands. On the other hand, digestive glands showed approximately 6 times more CAT specific activity than gills. Iron storage proteins were identified in gill extracts from all experimental conditions mussels. However, in digestive gland extracts only fresh collected mussels and after 2 weeks in FeSO4 showed the presence of iron storage proteins. The differences between SOD, CAT specific activities and the presence of iron storage proteins in the examined tissues reflect dissimilar metabolic and antioxidant activities, as a result of tissue specificities and acclimatization conditions influences on the organism.

Longevity of animals under reactive oxygen species stress and disease susceptibility due to global warming

The world is projected to experience an approximate doubling of atmospheric CO₂ concentration in the next decades. Rise in atmospheric CO₂ level as one of the most important reasons is expected to contribute to raise the mean global temperature 1.4 °C-5.8 °C by that time. A survey from 128 countries speculates that global warming is primarily due to increase in atmospheric CO₂ level that is produced mainly by anthropogenic activities. Exposure of animals to high environmental temperatures is mostly accompanied by unwanted acceleration of certain biochemical pathways in their cells. One of such examples is augmentation in generation of reactive oxygen species (ROS) and subsequent increase in oxidation of lipids, proteins and nucleic acids by ROS. Increase in oxidation of biomolecules leads to a state called as oxidative stress (OS). Finally, the increase in OS condition induces abnormality in physiology of animals under elevated temperature. Exposure of animals to rise in habitat temperature is found to boost the metabolism of animals and a very strong and positive correlation exists between metabolism and levels of ROS and OS. Continuous induction of OS is negatively correlated with survivability and longevity and positively correlated with ageing in animals. Thus, it can be predicted that continuous exposure of animals to acute or gradual rise in habitat temperature due to global warming may induce OS, reduced survivability and longevity in animals in general and poikilotherms in particular. A positive correlation between metabolism and temperature in general and altered O₂ consumption at elevated temperature in particular could also increase the risk of experiencing OS in homeotherms. Effects of global warming on longevity of animals through increased risk of protein misfolding and disease susceptibility due to OS as the cause or effects or both also cannot be ignored. Therefore, understanding the physiological impacts of global warming in relation to longevity of animals will become very crucial challenge to biologists of the present millennium.

Investigating the Conformational Structure and Potential Site Interactions of SOD Inhibitors on Ec-SOD in Marine Mud Crab Scylla serrata: A Molecular Modeling Approach

Superoxide dismutases (SODs) act as a first line of the enzymatic antioxidant defense system to control cellular superoxide anion toxicity. Previously, several inhibitors have been widely identified and catalogued for inhibition of SOD activity; however, still the information about the mechanism of interaction and points toward the inhibitor interactions in structures of SODs in general and in extracellular (Ec)-SOD in particular is still in naive. In the present research, we present an insight to elucidate the molecular basis of interactions of SOD inhibitors with Ec-SOD in mud crab Scylla serrata using molecular modeling and docking approaches. Different inhibitors of SOD such as hydrogen peroxide [Formula: see text], potassium cyanide, sodium dodecyl sulfate (SDS), [Formula: see text]-mercaptoethanol and dithiocarbamate were screened to understand the potential sites that may act as sites for cleavage or blocking in the protein. SOD-SDS and [Formula: see text] complex interactions indicate residues Pro72 and Asp102 of the predicted crab Ec-SOD as common targets. The GOLD result indicates that Pro72, Asp102 and Thr103 are commonly acting as the site of interaction in Ec-SOD of S. serrata with SOD inhibitors. For the first time, the results of this study provide an insight into the structural properties of Ec-SOD of S. serrata and define the possible involvements between the amino acids present in its active sites, i.e., in the regions from 70 to 84 and from 101 to 103 and different inhibitors.

Interaction model of steviol glycosides from Stevia rebaudiana (Bertoni) with sweet taste receptors: A computational approach

Docking studies were performed on natural sweeteners from Stevia rebaudiana by constructing homology models of T1R2 and T1R3 subunits of human sweet taste receptors. Ramachandran plot, PROCHECK results and ERRAT overall quality factor were used to validate the quality of models. Furthermore, docking results of steviol glycosides (SG's) were correlated significantly with data available in the literature which enabled to predict the exact sweetness rank order of SG's. The binding pattern indicated that Asn 44, Ans 52, Ala 345, Pro 343, Ile 352, Gly 346, Gly 47, Ala 354, Ser 336, Thr 326 and Ser 329 are the main interacting amino acid residues in case of T1R2 and Arg 56, Glu 105, Asp 215, Asp 216, Glu 148, Asp 258, Lys 255, Ser 104, Glu 217, Leu 51, Arg 52 for T1R3, respectively. Amino acids interact with SG's mainly by forming hydrogen bonds with the hydroxyl group of glucose moieties. Significant variation in docked poses of all the SG's were found. In this study, we have proposed the mechanism of the sweetness of the SG's in the form of multiple point stimulation model by considering the diverse binding patterns of various SG's, as well as their structural features. It will give further insight in understanding the differences in the quality of taste and will be used to improve the taste of SG's using semi-synthetic approaches.

Modulation of redox regulatory molecules and electron transport chain activity in muscle of air breathing fish Heteropneustes fossilis under air exposure stress

Responses of redox regulatory system to long-term survival (>18 h) of the catfish Heteropneustes fossilis in air are not yet understood. Lipid and protein oxidation level, oxidant (H2O2) generation, antioxidative status (levels of superoxide dismutase, catalase, glutathione peroxidase and reductase, ascorbic acid and non-protein sulfhydryl) and activities of respiratory complexes (I, II, III and IV) in mitochondria were investigated in muscle of H. fossilis under air exposure condition (0, 3, 6, 12 and 18 h at 25 °C). The increased levels of both H2O2 and tissue oxidation were observed due to the decreased activities of antioxidant enzymes in muscle under water deprivation condition. However, ascorbic acid and non-protein thiol groups were the highest at 18 h air exposure time. A linear increase in complex II activity with air exposure time and an increase up to 12 h followed by a decrease in activity of complex I at 18 h were observed. Negative correlation was observed for complex III and V activity with exposure time. Critical time to modulate the above parameters was found to be 3 h air exposure. Dehydration induced oxidative stress due to modulation of electron transport chain and redox metabolizing enzymes in muscle of H. fossilis was clearly observed. Possible contribution of redox regulatory system in muscle tissue of the fish for long-term survival in air is elucidated. Results of the present study may be useful to understand the redox metabolism in muscle of fishes those are exposed to air in general and air breathing fishes in particular.

Antioxidant and oxidative stress parameters in brain of Heteropneustes fossilis under air exposure condition; role of mitochondrial electron transport chain

Many fishes are exposed to air in their natural habitat or during their commercial handling. In natural habitat or during commercial handling, the cat fish Heteropneustes fossilis is exposed to air for >24h. Data on its oxidative metabolism in the above condition are not available. Oxidative stress (OS) indices (lipid and protein oxidation), toxic reactive oxygen species (ROS: H2O2) generation, antioxidative status (levels of superoxide dismutase, catalase, glutathione peroxidase and reductase, ascorbic acid and non-protein sulfhydryl) and activities of electron transport chain (ETC) enzymes (complex I-IV) were investigated in brain tissue of H. fossilis under air exposure condition (0, 3, 6, 12 and 18 h at 25°C). Decreased activities of antioxidant (except catalase) and ETC enzymes (except complex II) with increased H2O2 and OS levels were observed in the tissue under water deprivation condition. Positive correlation was observed for complex II activity and non-protein thiol groups with time period of air exposure. The critical time period to induce OS and to reduce most of the studied antioxidant level in brain was found to be 3-6h air exposure. The data can be useful to minimize the stress generated during commercial handling of the live fishes those exposed to air in general and H. fossilis in particular.