Biological regulatory network analysis for targeting the mitochondrial calcium uniporter (MCU) mediated calcium (Ca2+) transport in neurodegenerative disorders.

Calcium (Ca2+) has been observed as the most important ion involved in a series of cellular processes and its homeostasis is critical for normal cellular functions. Mitochondrial calcium uniporter (MCU) complex has been recognized as the most important calcium-specific channel located in the inner mitochondrial membrane and is one of the major players in maintaining the Ca2+ homeostasis by transporting Ca2+ across the mitochondrial membrane. Furthermore, dysregulation of the mitochondrial Ca2+ homeostasis has been orchestrated to neurodegenerative response. This necessitates quantitative evaluation of the MCU-dependent mROS production and subsequent cellular responses for more specific therapeutic interventions against neurodegenerative disorders. Towards this goal, here we present a biological regulatory network of MCU to dynamically simulate the MCU-mediated ROS production and its response in neurodegeneration. Previously, ruthenium complex RuRed and its derivatives have been reported to show low nM to high µM potency against MCU to maintain cytosolic Ca2+ (cCa2+) homeostasis by modulating mitochondrial Ca2+ (mCa2+) uptake. Therefore, structural modeling and dynamic simulation of MCU pore-forming subunit is performed to probe the interaction profiling of previously reported Ru265 and its derivatives compounds with MCU. The current study highlighted MCU as a potential drug target in neurodegenerative disorders. Furthermore, ASP261 and GLU264 amino acid residues in DIME motif of MCU pore-forming subunits are identified as crucial for modulating the activity of MCU in neurodegenerative disorders.

Arresting the biosynthesis of Lipid A to hinder Escherichia coli and Pseudomonas aeruginosa through fatty diglyceride.

Lipid A is a fragment of lipopolysaccharide (LPS) in gram-negative bacteria such as Escherichia coli and Pseudomonas aeruginosa; hence inhibition of its biosynthesis is one of the plausible ways of preventing such bacteria from growth and thus preventing gastrointestinal diseases caused by Escherichia coli and pseudomonas aeruginosa. This research revolves around the development of antibiotic glyceride derivatives for the inhibition of the biosynthesis of lipid A. To target the enzymes involved in the biosynthesis of lipid A, four N,N-dimethylaminobenzoate moiety containing fatty diglyceride derivatives were synthesized through a multi-step synthetic scheme starting from glycerol. The molecular structure of the targeted molecules and synthesized intermediates in the synthetic scheme were confirmed by detailed structural analysis through 1N-NMR, mass and IR spectroscopic techniques. Antibacterial activity was evaluated against the gram-negative bacteria (Escherichia coli and Pseudomonas aeruginosa). The derivatives also underwent docking analysis on the pdb's of enzymatic catalysts involved in the biosynthesis of lipid A using AutoDock Vina package. All synthesized fatty esters gave good antibacterial activity and binding energy upto -7 kcal/mol in the docking analysis. A structure-property relationship was established between alkyl chain lengths of diglycerides and their resultant binding energies. These molecules and their resultant activity can assist in further designing and retrosynthesis of molecular derivatives of drug molecules with lipid A biosynthesis as target for its inhibition.

Synthesis, Characterization, Biological Evaluation, and In Silico Studies of Imidazolium-, Pyridinium-, and Ammonium-Based Ionic Liquids Containing n-Butyl Side Chains.

Ionic liquids (ILs) have emerged as active pharmaceutical ingredients because of their excellent antibacterial and biological activities. Herein, we used the green-chemistry-synthesis procedure, also known as the metathesis method, to develop three series of ionic liquids using 1-methyl-3-butyl imidazolium, butyl pyridinium, and diethyldibutylammonium as cations, and bromide (Br-), methanesulfonate (CH3SO3-), bis(trifluoromethanesulfonyl)imide (NTf2-), dichloroacetate (CHCl2CO2-), tetrafluoroborate (BF4-), and hydrogen sulfate (HSO4-) as anions. Spectroscopic methods were used to validate the structures of the lab-synthesized ILs. We performed an agar well diffusion assay by using pathogenic bacteria that cause various infections (Escherichia coli; Enterobacter aerogenes; Klebsiella pneumoniae; Proteus vulgaris; Pseudomonas aeruginosa; Streptococcus pneumoniae; Streptococcus pyogenes) to scrutinize the in vitro antibacterial activity of the ILs. It was established that the nature and unique combination of the cations and anions were responsible for the antibacterial activity of the ILs. Among the tested ionic liquids, the imidazolium cation and NTf2- and HSO4- anions exhibited the highest antibacterial activity. The antibacterial potential was further investigated by in silico studies, and it was observed that bis(trifluoromethanesulfonyl)imide (NTf2-) containing imidazolium and pyridinium ionic liquids showed the maximum inhibition against the targeted bacterial strains and could be utilized in antibiotics. These antibacterial activities float the ILs as a promising alternative to the existing antibiotics and antiseptics.

A comparative evaluation of antibacterial activities of imidazolium-, pyridinium-, and phosphonium-based ionic liquids containing octyl side chains.

Antibacterial activity is an essential property of ionic liquids. In this work, a comprehensive study has been performed on the antibacterial activity of ionic liquids to be utilized for further research and applications. Eighteen ionic liquids viz. Octyl Imidazolium, octyl Pyridinium, quaternary phosphonium-based cations containing bromide, sodium methane sulphonates, bis(trifluoromethane sulfonyl) imide, dichloroacetate, tetrafluoroborate, hydrogen sulfate were prepared and characterized with the help of different spectroscopic techniques. All these samples of ionic liquids were tested for their antibacterial activity against the most commonly occurring bacteria in the environment, i.e., Enterobacter aerogenes (E. aerogenes), Proteus vulgaris (P. vulgaris), Klebsiella pneumoniae (K. pneumoniae), Pseudomonas aeruginosa (P. aeruginosa), Escherichia coli (E. coli), and Streptococcus pyogenes (S. pyogenes). Most of the ionic liquids show good antibacterial properties, and imidazolium-based ionic liquids were even more antibacterial as compared to positive control. It was observed that a unique combination of cation and anion is essential to achieve desired antibacterial properties. The mechanism of antibacterial activity was further investigated using density functional theory calculations. A good correlation was found between experimental and theoretical studies.

Colorimetric chromophoric rapid detection of SARS-CoV-2 through breath analysis.

Early and rapid detection of SARS-CoV-2 in an infected person is one fundamental part of the strategy against the spread of this virus. As of now, the usual practice is to carry out polymerase chain reaction (PCR) test which provides results in 24-48 hours. Hence, there exists a crucial need for rapid and immediate screening of people suspected to be infected. Presence of volatile organic compounds (VOCs) in the exhaled breath can be one such prospect for detection of virus. In this paper, we have designed chromophoric adducts of VOC's in the exhaled breath that can be formed for colorimetric detection of SARS-CoV-2. We noted the bathochromic shift in λ (nm) of VOC molecules upon chromophore formation for colorimetric detection. If adapted, this research work will result in low cost solution to the requirement of immediate detection of SARS-CoV-2, hence cost and time of testing will be reduced, compared to PCR and antibodies tests. Also VOC's detection in early stage of infection where symptoms are not visible can be advantageous.

Comparison of HRCT Chest and RT-PCR in Diagnosis of COVID-19.

OBJECTIVE: To compare the diagnostic accuracies of HRCT chest and RT-PCR results in diagnosis of coronavirus disease (COVID-19) in a tertiary care hospital in Lahore. STUDY DESIGN: Descriptive study. PLACE AND DURATION OF STUDY: Department of Radiology and Central Research Lab, Lahore General Hospital, Lahore, from April to July, 2020. METHODOLOGY: Patients aged 18 to 83 years, who had clinically suspected symptoms of COVID-19 (fever, cough/sore throat or shortness of breath) presenting in outpatient or emergency department, were included. These patients had their HRCT chest conducted from Radiology Department and RT-PCR performed at Central Research Lab. These data were retrieved from electronic system of PACS. Results were categorised into positive and negative findings for COVID-19. Diagnostic accuracies of HRCT chest and first RT-PCR along with 95% confidence interval were calculated. RESULTS: A total of 94 patients, 55 (58.5%) males and 39 (41.5%) were females. Out of them, 83% patients had positive HRCT chest findings of COVID-19, 17% had negative HRCT chest findings; while 40.4% had positive and 59.6% had negative first PCR. Among the repeat second PCR, 19.6% had negative, 1.8% had positive PCR results; while 78.6% patients didn't undergo repeat PCR. The sensitivity, specificity, NPV, PPV and accuracy of HRCT chest was 92%, 23%, 81%, 45%, and 51%; while of first RT-PCR was 45%, 81%, 23%, 92% and 51%, respectively. CONCLUSION: The sensitivity of HRCT chest is higher (92%) as compared to first RT-PCR (45%). Key Words: COVID-19, RT-PCR, HRCT chest, Sensitivity, Specificity.

Unraveling the Way Acetaldehyde is Formed from Acetylene: A Study Based on DFT.

Acetylene hydratase (AH) of Pelobacter acetylenicus is a tungsten (W)-containing iron-sulfur enzyme that catalyzes the transformation of acetylene to acetaldehyde, the exact/true reaction mechanism of which is still in question. Scientists utilized different computational approaches to understand the reaction mechanism of acetylene hydration. Some identified it as a multistep (4-16) process that starts with the displacement of a water molecule present at the active site of AH with acetylene. However, some said that there is no need to displace water with acetylene at the active site of AH. As the reaction mechanism for the conversion of acetylene to acetaldehyde is still controversial and needs to be investigated further, DFT studies were performed on the model complexes derived from the native protein X-ray crystal structure of AH. Based on the computational results, here we are proposing the nucleophilic reaction mechanism where the water (Wat1424) molecule is coordinated to the W center and Asp13 is assumed to be in an anionic form. The Wat1424 molecule is activated by W and then donates one of its protons to the anionic Asp13, forming the W-bound hydroxide and protonated Asp13. The W-bound hydroxide then attacks the C1 atom of acetylene together with the transfer of a proton from Asp13 to its C2 atom, resulting in the formation of a vinyl alcohol intermediate complex. The energy barrier associated with this step is 14.4 kcal/mol. The final, rate-limiting, step corresponds to the tautomerization of the vinyl alcohol intermediate to acetaldehyde via intermolecular assistance of two water molecules, associated with an energy barrier of 18.9 kcal/mol. Also, the influence of the metal on the hydration of acetylene is studied when W is replaced with Mo.

Comparison of HRCT Chest and RT-PCR in Diagnosis of COVID-19.

OBJECTIVE: To compare the diagnostic accuracies of HRCT chest and RT-PCR results in diagnosis of coronavirus disease (COVID-19) in a tertiary care hospital in Lahore. STUDY DESIGN: Descriptive study. PLACE AND DURATION OF STUDY: Department of Radiology and Central Research Lab, Lahore General Hospital, Lahore, from April to July, 2020. METHODOLOGY: Patients aged 18 to 83 years, who had clinically suspected symptoms of COVID-19 (fever, cough/sore throat or shortness of breath) presenting in outpatient or emergency department, were included. These patients had their HRCT chest conducted from Radiology Department and RT-PCR performed at Central Research Lab. These data were retrieved from electronic system of PACS. Results were categorised into positive and negative findings for COVID-19. Diagnostic accuracies of HRCT chest and first RT-PCR along with 95% confidence interval were calculated. RESULTS: A total of 94 patients, 55 (58.5%) males and 39 (41.5%) were females. Out of them, 83% patients had positive HRCT chest findings of COVID-19, 17% had negative HRCT chest findings; while 40.4% had positive and 59.6% had negative first PCR. Among the repeat second PCR, 19.6% had negative, 1.8% had positive PCR results; while 78.6% patients didn't undergo repeat PCR. The sensitivity, specificity, NPV, PPV and accuracy of HRCT chest was 92%, 23%, 81%, 45%, and 51%; while of first RT-PCR was 45%, 81%, 23%, 92% and 51%, respectively. CONCLUSION: The sensitivity of HRCT chest is higher (92%) as compared to first RT-PCR (45%). Key Words: COVID-19, RT-PCR, HRCT chest, Sensitivity, Specificity.

Effect of molybdenum and tungsten on the reduction of nitrate in nitrate reductase, a DFT study.

The molybdenum and tungsten active site model complexes, derived from the protein X-ray crystal structure of the first W-containing nitrate reductase isolated from Pyrobaculum aerophilum, were computed for nitrate reduction at the COSMO-B3LYP/SDDp//B3LYP/Lanl2DZ(p) energy level of density functional theory. The molybdenum containing active site model complex (Mo-Nar) has the largest activation energy (34.4 kcal/mol) for the oxygen atom transfer from the nitrate to the metal center as compared to the tungsten containing active site model complex (W-Nar) (12.0 kcal/mol). Oxidation of the educt complex is close to thermoneutral (-1.9 kcal/mol) for the Mo active site model complex but strongly exothermic (-34.7 kcal/mol) for the W containing active site model complex, however, the MVI to MIV reduction requires equal amount of reductive power for both metal complexes, Mo-Nar or W-Nar.