Effect of halides in the electrochemical treatment of distillery effluent

Electrochemical treatment can solve the problems arising due to effluents and offer an effective alternative to the existing methods. An undivided static electrolyser was charged with distillery effluent and the organics were oxidized electrochemically. Anodized graphite plate anodes and graphite cathodes were used for the treatment of distillery effluent. The effect of pH and current density on the treatment was studied. Sodium fluoride, sodium chloride and sodium bromide were chosen as electrolyte and their influence was found out. Complete decolorization has been observed in all cases. A maximum of 93.5% of biological oxygen demand reduction, 85.2% of chemical oxygen demand reduction and 98.0% absorbance reduction were obtained in the presence of sodium chloride as supporting electrolyte. Probable mechanism was also proposed for the oxidation of organics present in the effluent.

Structure-Based Virtual Screening and Biochemical Validation to Discover a Potential Inhibitor of the SARS-CoV-2 Main Protease

The recent pandemic caused by SARS-CoV-2 has led the world to a standstill, causing a medical and economic crisis worldwide. This crisis has triggered an urgent need to discover a possible treatment strategy against this novel virus using already-approved drugs. The main protease (Mpro) of this virus plays a critical role in cleaving the translated polypeptides that makes it a potential drug target against COVID-19. Taking advantage of the recently discovered three-dimensional structure of Mpro, we screened approved drugs from the Drug Bank to find a possible inhibitor against Mpro using computational methods and further validating them with biochemical studies. The docking and molecular dynamics study revealed that DB04983 (denufosol) showed the best glide docking score, -11.884 kcal/mol, and MM-PBSA binding free energy, -10.96 kcal/mol. Cobicistat, cangrelor (previous computational studies in our lab), and denufosol (current study) were tested for the in vitro inhibitory effects on Mpro. The IC50 values of these drugs were ∼6.7 μM, 0.9 mM, and 1.3 mM, respectively, while the values of dissociation constants calculated using surface plasmon resonance were ∼2.1 μM, 0.7 mM, and 1.4 mM, respectively. We found that cobicistat is the most efficient inhibitor of Mpro both in silico and in vitro. In conclusion, cobicistat, which is already an FDA-approved drug being used against HIV, may serve as a good inhibitor against the main protease of SARS-CoV-2 that, in turn, can help in combating COVID-19, and these results can also form the basis for the rational structure-based drug design against COVID-19.

Computationally Guided Identification of Novel Mycobacterium tuberculosis GlmU Inhibitory Leads, Their Optimization, and in Vitro Validation

Mycobacterium tuberculosis (Mtb) infections are causing serious health concerns worldwide. Antituberculosis drug resistance threatens the current therapies and causes further need to develop effective antituberculosis therapy. GlmU represents an interesting target for developing novel Mtb drug candidates. It is a bifunctional acetyltransferase/uridyltransferase enzyme that catalyzes the biosynthesis of UDP-N-acetyl-glucosamine (UDP-GlcNAc) from glucosamine-1-phosphate (GlcN-1-P). UDP-GlcNAc is a substrate for the biosynthesis of lipopolysaccharide and peptidoglycan that are constituents of the bacterial cell wall. In the current study, structure and ligand based computational models were developed and rationally applied to screen a drug-like compound repository of 20,000 compounds procured from ChemBridge DIVERSet database for the identification of probable inhibitors of Mtb GlmU. The in vitro evaluation of the in silico identified inhibitor candidates resulted in the identification of 15 inhibitory leads of this target. Literature search of these leads through SciFinder and their similarity analysis with the PubChem training data set (AID 1376) revealed the structural novelty of these hits with respect to Mtb GlmU. IC50 of the most potent identified inhibitory lead (5810599) was found to be 9.018 ± 0.04 μM. Molecular dynamics (MD) simulation of this inhibitory lead (5810599) in complex with protein affirms the stability of the lead within the binding pocket and also emphasizes on the key interactive residues for further designing. Binding site analysis of the acetyltransferase pocket with respect to the identified structural moieties provides a thorough analysis for carrying out the lead optimization studies.

Escherichia coli N-Acetylglucosamine-1-Phosphate-Uridyltransferase/Glucosamine-1-Phosphate-Acetyltransferase (GlmU) Inhibitory Activity of Terreic Acid Isolated from Aspergillus terreus

Secondary metabolite of Aspergillus terreus, terreic acid, is a reported potent antibacterial that was identified more than 60 years ago, but its cellular target(s) are still unknown. Here we screen its activity against the acetyltransferase domain of a bifunctional enzyme, Escherichia coli N-acetylglucosamine-1-phosphate-uridyltransferase/glucosamine-1-phosphate-acetyltransferase (GlmU). An absorbance-based assay was used to screen terreic acid against the acetyltransferase activity of E. coli GlmU. Terreic acid was found to inhibit the acetyltransferase domain of E. coli GlmU with an IC50 of 44.24 ± 1.85 µM. Mode of inhibition studies revealed that terreic acid was competitive with AcCoA and uncompetitive with GlcN-1-P. It also exhibited concentration-dependent killing of E. coli ATCC 25922 up to 4× minimum inhibitory concentration and inhibited the growth of biofilms generated by E. coli. Characterization of resistant mutants established mutation in the acetyltransferase domain of GlmU. Terreic acid was also found to be metabolically stable in the in vitro incubations with rat liver microsome in the presence of a NADPH regenerating system. The studies reported here suggest that terreic acid is a potent antimicrobial agent and support that E. coli GlmU acetyltransferase is a molecular target of terreic acid, resulting in its antibacterial activity.

BA.1, BA.2 and BA.2.75 variants show comparable replication kinetics, reduced impact on epithelial barrier and elicit cross-neutralizing antibodies

The Omicron variant of SARS-CoV-2 is capable of infecting unvaccinated, vaccinated and previously-infected individuals due to its ability to evade neutralization by antibodies. With multiple sub-lineages of Omicron emerging in the last 12 months, there is inadequate information on the quantitative antibody response generated upon natural infection with Omicron variant and whether these antibodies offer cross-protection against other sub-lineages of Omicron variant. In this study, we characterized the growth kinetics of Kappa, Delta and Omicron variants of SARS-CoV-2 in Calu-3 cells. Relatively higher amounts infectious virus titers, cytopathic effect and disruption of epithelial barrier functions was observed with Delta variant whereas infection with Omicron sub-lineages led to a more robust induction of interferon pathway, lower level of virus replication and mild effect on epithelial barrier. The replication kinetics of BA.1, BA.2 and BA.2.75 sub-lineages of the Omicron variant were comparable in cell culture and natural infection in a subset of individuals led to a significant increase in binding and neutralizing antibodies to the Delta variant and all the three sub-lineages of Omicron but the level of neutralizing antibodies were lowest against the BA.2.75 variant. Finally, we show that Cu2+, Zn2+ and Fe2+ salts inhibited in vitro RdRp activity but only Cu2+ and Fe2+ inhibited both the Delta and Omicron variants in cell culture. Thus, our results suggest that high levels of interferons induced upon infection with Omicron variant may counter virus replication and spread. Waning neutralizing antibody titers rendered subjects susceptible to infection by Omicron variants and natural Omicron infection elicits neutralizing antibodies that can cross-react with other sub-lineages of Omicron and other variants of concern.

An Intelligent Operator for Genetic Fuzzy Rule Based System

This paper proposes a modified form of operator based on Particle Swarm Optimization (PSO) for designing Genetic Fuzzy Rule Based System (GFRBS). The usual procedure of velocity updating in PSO is modified by calculating the velocity using chromosome’s individual best value and global best value based on an updating probability without considering the inertia weight, old velocity and constriction factors. This kind of calculation brings intelligent information sharing mechanism and memory capability to Genetic Algorithm (GA) and can be easily implemented along with other genetic operators. The performance of the proposed operator is evaluated using ten publicly available bench mark data sets. Simulation results show that the proposed operator introduces new material into the population, thereby allows faster and more accurate convergence without struck into a local optima. Statistical analysis of the experimental results shows that the proposed operator produces a classifier model with minimum number of rules and higher classification accuracy.

Identification and characterization of novel small molecule inhibitors of the acetyltransferase activity of Escherichia coli N-acetylglucosamine-1-phosphate-uridyltransferase/glucosamine-1-phosphate-acetyltransferase (GlmU)

This study aims at identifying novel chemical scaffolds as inhibitors specific to the acetyltransferase domain of a bifunctional enzyme, Escherichia coli GlmU, involved in the cell wall biosynthesis of Gram-negative organisms. A two-pronged approach was used to screen a 50,000 small-molecule library. Using the first approach, the library was in silico screened by docking the library against acetyltransferase domain of E. coli GlmU studies. In the second approach, complete library was screened against Escherichia coli ATCC 25922 to identify the whole cell active compounds. Active compounds from both the screens were screened in a colorimetric absorbance-based assay to identify inhibitors of acetyltransferase domain of E. coli GlmU which resulted in the identification of 1 inhibitor out of 56 hits identified by in silico screening and 4 inhibitors out of 35 whole cell active compounds on Gram-negative bacteria with the most potent inhibitor showing IC50 of 1.40 ± 0.69 μM. Mode of inhibition studies revealed these inhibitors to be competitive with AcCoA and uncompetitive with GlcN-1-P. These selected inhibitors were also tested for their antibacterial and cytotoxic activities. Compounds 5175178 and 5215319 exhibited antibacterial activity that co-related with GlmU inhibition. These compounds, therefore, represent novel chemical scaffolds targeting acetyltransferase activity of E. coli GlmU.

Fuzzy-rough-neural-based f-information for gene selection and sample classification

The greatest restriction in estimating the information measure for microarray data is the continuous nature of gene expression values. The traditional criterion function of f-information discretises the continuous gene expression value for calculating the probability function during gene selection. This leads to loss of biological meaning of microarray data and results in poor classification accuracy. To overcome this difficulty, the concepts of fuzzy and rough set are combined to redefine the criterion functions of f-information and are used to form candidate genes from which informative genes are selected using neural network. The performance of the proposed Fuzzy-Rough-Neural-based f-Information (FRNf-I) is evaluated using ten gene expression datasets. Simulation results show that the proposed approach compute f-information measure easily without discretisation. Statistical analysis of the test result shows that the proposed FRNf-I selects comparatively less number of genes and more classification accuracy than the other approaches reported in the literature.

Potassium-induced partial inhibition of lactoperoxidase: structure of the complex of lactoperoxidase with potassium ion at 2.20 Å resolution

Lactoperoxidase, a heme-containing glycoprotein, catalyzes the oxidation of thiocyanate by hydrogen peroxide into hypothiocyanite which acts as an antibacterial agent. The prosthetic heme moiety is attached to the protein through two ester linkages via Glu258 and Asp108. In lactoperoxidase, the substrate-binding site is formed on the distal heme side. To study the effect of physiologically important potassium ion on the structure and function of lactoperoxidase, the fresh protein samples were isolated from yak (Bos grunniens) colostrum and purified to homogeneity. The biochemical studies with potassium fluoride showed a significant reduction in the catalytic activity. Lactoperoxidase was crystallized using 200 mM ammonium nitrate and 20% PEG-3350 at pH 6.0. The crystals of LPO were soaked in the solution of potassium fluoride and used for the X-ray intensity data collection. Structure determination at 2.20 Å resolution revealed the presence of a potassium ion in the distal heme cavity. Structure determination further revealed that the propionic chain attached to pyrrole ring C of the heme moiety, was disordered into two components each having an occupancy of 0.5. One component occupied a position similar to the normally observed position of propionic chain while the second component was found in the distal heme cavity. The potassium ion in the distal heme cavity formed five coordinate bonds with two oxygen atoms of propionic moiety, N^ε2 atom of His109 and two oxygen atoms of water molecules. The presence of potassium ion in the distal heme cavity hampered the catalytic activity of lactoperoxidase.

Acclimatory response to hydrogen peroxide and glutathione under salt-boron stress through their impact on mineral nutrition and antioxidant defense system in pigeonpea (Cajanus cajan L.)

Investigations were carried out on a salt tolerant (Manak, H77-216) and a comparatively salt sensitive (ICPL 88039) genotypes of pigeonpea (Cajanus cajan L. Millsp.) under NaCl, B and NaCl + B stress to examine the acclimatory response to H2O2, glutathione and H2O2 + glutathione through their effect on mineral nutrition, morpho-physiological parameters and antioxidant defense system. Both B and NaCl alone and their combinations had deleterious effect on dry biomass of plumule, enhanced relative stress injury (RSI), lipid peroxidation with concomitant increase in Na, Cl and B contents. However it did not bear any correlation with osmotic potential of plumule and K contents. Antioxidative enzymes like superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), peroxidase (POX) and glutathione reductase (GR) also decreased with salt, B and salt + B treatments. However contents of H2O2 enhanced and that of ascorbate declined under aforementioned treatments. These injurious effects are partially alleviated by exogenous application of H2O2; glutathione (GSH) and H2O2 + GSH treatments. The role of H2O2 and GSH in the present study is suggestive of triggering multifunctional signal transduction in plant defense mechanisms to prevent cellular oxidation, membrane injury, lipid peroxidation and protein enzyme inactivation.

Biophysical Characterization of Type III Pantothenate Kinase (PanK) from Acinetobacter baumannii

BACKGROUND

Type-III Pantothenate kinase from the multi drug resistant bacteria, Acinetobacter baumannii (AbPanK) catalyzes the first step of the essential Coenzyme A biosynthesis pathway. AbPanK is an attractive drug target against the bacteria since it is an essential enzyme and its structure is significantly different from the human PanK.

METHODS

AbPanK was cloned, expressed, purified and crystallized. A good quality single crystal was used for X-ray intensity data collection. Dynamic light scattering was done for calculating the hydrodynamic radii and its oligomeric nature in the solution. Binding studies of this protein with its two substrates, Pantothenate and ATP were done using spectrofluorometer.

RESULTS

Our results indicated that AbPanK shows a strong affinity with pantothenate with dissociation constant of 1.2 x 10- 8 M and moderate affinity towards ATP of 3.7x 10-3 M. This fact was further substantiated by the calculations of Km of both substrates using kinase assay kit. Dynamic light scattering studies have shown that it exists as homogenous solution with hydrodynamic radii corresponding to the molecular weight of 29.55 kDa. A low-resolution X-ray intensity data set was collected, which shows that AbPank crystallizes in P2 space group with cell dimensions of a= 165 Å, b= 260 Å, and, c= 197 Å and α= 90.0, β= 113.60, γ= 90.0.

DISCUSSION

Recombinant Pantothenate kinase from Acinetobacter baumannii was purified to homogeneity and crystallized. The enzyme exhibits very low sequence identity (28%) to other corresponding enzymes.

CONCLUSION

The recombinant enzyme was active and its binding affinities with its substrates pantothenate and ATP have been studied. This information would be very useful while designing the inhibitors of this enzyme in order to fight bacterial infections associated to this pathogen.

Dengue fever outbreaks in two villages of Dharmapuri district in Tamil Nadu

BACKGROUND & OBJECTIVES

Dengue fever is an important public health problem in India. In recent years this disease has extended to rural areas also due to rapid urbanization. In Tamil Nadu, fever outbreaks were reported in two villages of Dharmapuri district during May and September 2001 with clinical symptoms suggestive of dengue fever. Epidemiological, virological and entomological investigations were carried out in these two villages to ascertain the etiology of the outbreaks.

METHODS

Paired serum samples were collected from febrile patients clinically suspected to have dengue and were tested for the presence of IgM antibodies to dengue virus by MAC ELISA. Samples were also tested by Dengue Duo IgM/IgG rapid strip. Surveys of larval and adult Aedes mosquitoes were carried out before and after anti-larval and anti-adult measures were implemented. Female Ae. aegypti mosquitoes collected in Mampatti village were tested individually for the presence of dengue-2 viral antigen by indirect immunofluorescence assay (IIFA). In addition, two pools of female Ae. aegypti mosquitoes were tested for the presence of dengue viral antigen by ELISA and then subjected to Toxo-IFA system for demonstration of dengue virus.

RESULTS

A total of 124 and 267 fever cases with clinical symptoms and signs suggestive of dengue were reported in Kadumuchandiram and Mampatti villages of Dharmapuri district, respectively. Serodiagnosis revealed that 13 of 31 and 14 of 52 patients tested were positive for dengue-2 virus by MAC ELISA in Kadumuchandiram and Mampatti villages respectively. Dengue Duo rapid strip test also detected 14 (of 31 tested) patients positive for dengue virus specific IgM antibodies in Kadumuchandiram village and 8 (of 12 tested) in Mampatti village. Application of temephos and fogging with pyrethrum 2 per cent extract were found to be effective against immatures and adults respectively. Both the pools of Ae. aegypti tested for the presence of dengue viral antigen were positive by ELISA and one mosquito (tested individually) was positive by IIFA. Supernatants of two pools were found to be positive for dengue-2 virus by Toxo-IFA.

INTERPRETATION & CONCLUSION

Virological and serological investigations confirmed that the outbreaks of fever were due to dengue virus infection. High breeding of Ae. aegypti in the study villages, detection of dengue-2 viral antigen and isolation of dengue-2 virus in Ae. aegypti mosquitoes confirmed the etiology.

Oxidative stress and metabolic control in non-insulin dependent diabetes mellitus

The aim of this study was to evaluate conjugated dienes in subjects with non-insulin-dependent diabetes mellitus (NIDDM) and its metabolic control. To achieve good metabolic control in addition to dietary management oral hypoglycemic agents such as glibenclamide, gliclazide and metformin were given to patients. Human plasma low-density lipoproteins (LDL) were delipidised and triglycerides (LDL-TG) and cholesterol esters (LDL-CE) were separated. Conjugated dienes in LDL-TG and LDL-CE of subjects with NIDDM (n = 90) and normal glucose tolerance (NGT) (n = 30) were measured using second derivative of uv absorption spectrum. Hypoglycemic agents lowered substantially concentration of cis, trans (c, t) and trans, trans (t, t) conjugated dienes in LDL-CE and LDL-TG. The duration of NIDDM has shown significant correlation (p < 0.001) with conjugated dienes in LDL-TG. Concentration of c, t and t, t-conjugated dienes in LDL-CE and LDL-TG were found significantly higher in subjects with NIDDM than NGT (p < 0.001). In conclusion, NIDDM, status of metabolic control and duration of diabetes have strong positive relation with oxidative stress.

Computational exploration of viral cell membrane structures for identifying novel therapeutic target

The membrane proteins of viruses play a critical role, and they shield viruses and takes biochemical mechanisms like sticking to the host cell membrane, merging with them, building new viruses, and breaking free. These steps make sure the virus can infect and multiply. But the membrane proteins of Nipah, Zika, SARS-CoV-2, and Hendra virus can cause special kinds of infections. Nipah and Hendra viruses use their fusion protein to join with the host cell membrane. Their glycoprotein interacts with host receptors. The matrix protein helps to build and support the virus structure. Zika virus relies on its envelope protein to attach and fuse with host cells. Its membrane protein keeps the viral envelope stable. SARS-CoV-2 uses its spike protein to enter host cells and its envelope protein helps assemble new viruses. The membrane protein gives structural stability whereas the nucleocapsid protein interacts with the RNA genome. These viral membranes contain various kinds of lipids and proteins and they make up about 30 % of the membrane area. Yet, scientists find it hard to predict their molecular structure and different biological characters. The coarse-grained molecular dynamics simulations, enhanced sampling methods, and various structural bioinformatics investigations on viral proteins provide reliable scientific data. These investigations reveal viral membrane proteins' structural features, movement patterns, and thermodynamic properties. These computer methods are vital for drug discovery because it allows researchers to find new compounds that target viral membrane proteins to prevent their functions.

Lipoprotein(a) and coronary heart disease in Indian population

OBJECTIVE

Present study was undertaken to evaluate the role of lipoprotein(a) in coronary heart disease (CHD) patients and its relationship with other established risk factors.

METHODS

Blood samples of 67 control patients (non-cardiovascular problems) and 222 CHD patients (> or = 4 weeks post myocardial infarction) were analyzed. Lipoprotein(a) was measured in serum samples by enzyme-linked immunosorbent assay utilizing rabbit polyclonal antibodies against purified human Lp(a). Step-wise linear discriminant analysis was used to find the important parameters to discriminate CHD and non-CHD subjects.

RESULTS

The LDL to HDL cholesterol ratio (p < 0.01) and serum level of lipoprotein(a) (p < 0.01) were significantly higher in CHD patients. Levels of lipoprotein(a) were found to be higher in females compared to males (p < 0.01). Positive family history of CHD did not show significant difference in Lp(a) levels. Lp(a) level in CHD patients with positive family history of NIDDM and hypertension was higher than in with negative family history.

CONCLUSION

Clinical significance of serum level of Lp(a) and albumin in determining the risk of CHD has been observed. Lp(a) alone could correctly discriminate a CHD individual from a control subjects by 95%. Estimating of Lp(a) together with albumin provided 99% correct discrimination between control and CHD patients. These results also suggest that Lp(a) together with malnutrition could be responsible for the increased incidence of CHD in Indians. It is also indicated that in females atherothrombogenic potential of lipoprotein(a) remains suppressed before menopause but after this stage women lose this advantage.