Genistein mitigates nitroglycerine-induced migraine: modulation of nitric oxide-mediated vasodilation and oxidative stress.

Migraine is a widespread brain condition described by frequent, recurrent episodes of incapacitating, moderate-to-severe headaches with throbbing pain that are usually one-sided. It is the 2nd most debilitating state lived with disability in terms of years, with a prevalence rate of 15-20%. Significant drops in estrogen levels have been associated with triggering acute migraine attacks in certain cases. Phytoestrogens are plant-derived compounds that resemble estrogen in structure, enabling them to imitate estrogen's functions in the body by attaching to estrogen receptors. Thus, the study was aimed to explore the protective effect of genistein against migraine. Moreover, the role of nitric oxide was also studied in the observed effect of genistein. Nitric oxide (NO) is implicated in migraine pathophysiology due to its role in promoting cerebral vasodilation and modulation of pain perception. Exploring L-NAME, a nitric oxide synthase inhibitor in migraine research helps scientists better understand the role of NO in migraine. Nitroglycerine treatment significantly increased the facial-unilateral head pain and spontaneous pain, as evidenced by the increased number of head scratching and groomings. Nitroglycerine treatment also induced anxiogenic behavior in mice. A significant reduction in the number of entries in the light phase and open arm, respectively. Biochemical analysis indicated a significant increase in inflammatory and oxidative stress in the nitroglycerin group. A significant increase and decrease in brain TBARS and GSH were observed with nitroglycerine treatment, respectively. Moreover, nitroglycerine treatment has uplifted the serum TNF-α level. Genistein (20 mg/kg) significantly mitigated the facial-unilateral head pain, spontaneous pain, photophobia, and anxiety-like behavior induced by nitroglycerine. Biochemical analysis showed that genistein (20 mg/kg) significantly abrogated the nitroglycerine-induced lipid peroxidation and increased serum TNF-α level. Genistein treatment also upregulated the brain GSH level and downregulated the serum TNF-α level. The L-NAME-mediated alleviation of the protective effect of genistein might be attributed to the vasodilatory effect of L-NAME. Conclusively, it can be suggested that genistein might provide relief from migraine pain by inhibiting nitric oxide-mediated vasodilation and oxidative stress.

Cancer-associated fibroblast-derived acetate promotes pancreatic cancer development by altering polyamine metabolism via the ACSS2-SP1-SAT1 axis.

The ability of tumour cells to thrive in harsh microenvironments depends on the utilization of nutrients available in the milieu. Here we show that pancreatic cancer-associated fibroblasts (CAFs) regulate tumour cell metabolism through the secretion of acetate, which can be blocked by silencing ATP citrate lyase (ACLY) in CAFs. We further show that acetyl-CoA synthetase short-chain family member 2 (ACSS2) channels the exogenous acetate to regulate the dynamic cancer epigenome and transcriptome, thereby facilitating cancer cell survival in an acidic microenvironment. Comparative H3K27ac ChIP-seq and RNA-seq analyses revealed alterations in polyamine homeostasis through regulation of SAT1 gene expression and enrichment of the SP1-responsive signature. We identified acetate/ACSS2-mediated acetylation of SP1 at the lysine 19 residue that increased SP1 protein stability and transcriptional activity. Genetic or pharmacologic inhibition of the ACSS2-SP1-SAT1 axis diminished the tumour burden in mouse models. These results reveal that the metabolic flexibility imparted by the stroma-derived acetate enabled cancer cell survival under acidosis via the ACSS2-SP1-SAT1 axis.

Modulation of Krüppel-like factors (KLFs) interaction with their binding partners in cancers through acetylation and phosphorylation.

Post-translational modifications (PTMs) of transcription factors regulate transcriptional activity and play a key role in essentially all biological processes and generate indispensable insight towards biological function including activity state, subcellular localization, protein solubility, protein folding, substrate trafficking, and protein-protein interactions. Amino acids modified chemically via PTMs, function as molecular switches and affect the protein function and characterization and increase the proteome complexity. Krüppel-like transcription factors (KLFs) control essential cellular processes including proliferation, differentiation, migration, programmed cell death and various cancer-relevant processes. We investigated the interactions of KLF group-2 members with their binding partners to assess the role of acetylation and phosphorylation in KLFs on their binding affinity. It was observed that acetylation and phosphorylation at different positions in KLFs have a variable effect on binding with specific partners. KLF2-EP300, KLF4-SP1, KLF6-ATF3, KLF6-JUN, and KLF7-JUN show stabilization upon acetylation or phosphorylation at variable positions. On the other hand, KLF4-CBP, KLF4-EP300, KLF5-CBP, KLF5-WWP1, KLF6-SP1, and KLF7-ATF3 show stabilization or destabilization due to acetylation or phosphorylation at variable positions in KLFs. This provides a molecular explanation of the experimentally observed dual role of KLF group-2 members as a suppressor or activator of cancers in a PTM-dependent manner.

Biosensor Assays Types and Their Roles Toward Ligand-Receptor Interactions in Drug Discovery.

Ligand-receptor interactions (LRIs) are the basis for all the biological processes taking place in living cells and have been exploited to develop and implement in medical field a number of highly sensitive biosensors for the detection of various biomarkers in complex biological fluids. Drug-target interactions, one of the LRIs, are important to understand the biological processes that further help in developing new and better therapeutic molecules. Biosensors based on these interactions give us an idea for the need of modification of existing drugs or to develop new drugs. Common approach to develop biosensors requires the labeling; however, label-free systems provide advantages in avoiding the chances of conformational changes, off-site labeling, and labeling-based hindrances, thus saving time and effort toward assay development. Preliminary drug screening assays are carried out in two-dimensional (2D) models, followed by animal models, which require huge capital investment to reach from bench-top to clinical trials, where only 21% of new compounds make way to phase-1 clinical trials. Three-dimensional culture or organoid culture or organ-on-chip technology has made way for predictive and complex in vitro approach that recapitulates human physiology and represents more similar in vivo behavior than 2D. Multiplexing and nanotechnology have remarkably enhanced the efficacy of biosensors and might lead to a generation of miniaturized biosensors and more than just point-of-care kits. This review provides in-depth analysis of different types of biosensor assays based on drug-target interactions, their advantages, and limitations based on cost, sensitivity, and selectivity and industrial applications.

Metabolic Rewiring by Loss of Sirt5 Promotes Kras-Induced Pancreatic Cancer Progression.

BACKGROUND & AIMS: SIRT5 plays pleiotropic roles via post-translational modifications, serving as a tumor suppressor, or an oncogene, in different tumors. However, the role SIRT5 plays in the initiation and progression of pancreatic ductal adenocarcinoma (PDAC) remains unknown. METHODS: Published datasets and tissue arrays with SIRT5 staining were used to investigate the clinical relevance of SIRT5 in PDAC. Furthermore, to define the role of SIRT5 in the carcinogenesis of PDAC, we generated autochthonous mouse models with conditional Sirt5 knockout. Moreover, to examine the mechanistic role of SIRT5 in PDAC carcinogenesis, SIRT5 was knocked down in PDAC cell lines and organoids, followed by metabolomics and proteomics studies. A novel SIRT5 activator was used for therapeutic studies in organoids and patient-derived xenografts. RESULTS: SIRT5 expression negatively regulated tumor cell proliferation and correlated with a favorable prognosis in patients with PDAC. Genetic ablation of Sirt5 in PDAC mouse models promoted acinar-to-ductal metaplasia, precursor lesions, and pancreatic tumorigenesis, resulting in poor survival. Mechanistically, SIRT5 loss enhanced glutamine and glutathione metabolism via acetylation-mediated activation of GOT1. A selective SIRT5 activator, MC3138, phenocopied the effects of SIRT5 overexpression and exhibited antitumor effects on human PDAC cells. MC3138 also diminished nucleotide pools, sensitizing human PDAC cell lines, organoids, and patient-derived xenografts to gemcitabine. CONCLUSIONS: Collectively, we identify SIRT5 as a key tumor suppressor in PDAC, whose loss promotes tumorigenesis through increased noncanonic use of glutamine via GOT1, and that SIRT5 activation is a novel therapeutic strategy to target PDAC.

Perspective on the Role of Antibodies and Potential Therapeutic Drugs to Combat COVID-19.

The sudden emergence of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing the coronavirus disease of 2019 (COVID-19) has brought the world to a standstill. Thousands of people across the globe are biting the dust with every passing day and yet more are being tested positive for the SARS-CoV-2 infection. In order to dispense this current crisis, numerous treatment options have been tried and tested and many more are still under scrutiny. The development of vaccines may help in the prevention of the global pandemic, however, there is still a need for the development of alternate approaches to combat the disease. In this review we highlight the new discoveries and furtherance in the antibody based therapeutic options and the potent drugs, with special emphasis on the development of the monoclonal and polyclonal antibodies and the repurposed drugs, which may prove to be of significant importance for the treatment of COVID-19, in the days to come. It is an attempt to evaluate the currently presented challenges so as to provide a scope for the ongoing research and assistance in the development of the effective therapeutic options against SARS-CoV-2.

Distinct Intramolecular Hydrogen Bonding Dictates Antimicrobial Action of Membrane-Targeting Amphiphiles.

As mechanisms underpinning the molecular interactions between membrane-targeting antimicrobials and Gram-negative bacterial membranes at atomistic scale remain elusive, we used cholic acid (CA)-derived amphiphiles with different hydrophobicities as model antimicrobials and assessed the effect of their conformational flexibility on antimicrobial activity. Relative to other hydrophobic counterparts, a compound with a hexyl chain (6) showed the strongest binding with the lipopolysaccharide (LPS) of Gram-negative bacterial membranes and acted as an effective antimicrobial. Biomolecular simulations, validated by complementary approaches, revealed that specific intramolecular hydrogen bonding imparts conformationally rigid character to compound 6. This conformational stability of compound 6 allows minimum but specific interactions of the amphiphile with LPS that are a sum of exothermic processes like electrostatic interactions, membrane insertion, and endothermic contributions from disaggregation of LPS. Therefore, our study reveals that a membrane-targeting mechanism with the help of conformationally selective molecules offers a roadmap for developing future therapeutics against bacterial infections.

A novel mutation alters the stability of PapA2 resulting in the complete abrogation of sulfolipids in clinical mycobacterial strains.

The analysis of whole genomes has revealed specific geographical distribution of Mycobacterium tuberculosis (Mtb) strains across the globe suggestive of unique niche dependent adaptive mechanisms. We provide an important correlation of a genome-based mutation to a molecular phenotype across two predominant clinical Mtb lineages of the Indian subcontinent. We have identified a distinct lineage specific mutation-G247C, translating into an alanine-proline conversion in the papA2 gene of Indo-oceanic lineage 1 (L1) Mtb strains, and restoration of cell wall sulfolipids by simple genetic complementation of papA2 from lineage 3 (L3) or from H37Rv (lineage 4-L4) attributed the loss of this glycolipid to this specific mutation in Indo-Oceanic L1 Mtb. The investigation of structure of Mtb PapA2 revealed a distinct nonribosomal peptide synthetase (NRPS) C domain conformation with an unconventional presence of a zinc binding motif. Surprisingly, the A83P mutation did not map to either the catalytic center in the N-terminal subdomain or any of the substrate-binding region of the protein. On the contrary, the inherent ability of mutant PapA2 to form insoluble aggregates and molecular simulations with the wild-type/mutant (Wt/mut) PapA2 purports an important role for the surface associated 83rd residue in protein conformation. This study demonstrates the importance of a critical structural residue in the papA2 protein of Mtb and helps establish a link between observed genomic alteration and its molecular consequence in the successful human pathogen Mtb. Significance We demonstrate the effect of a unique SNP in PapA2 gene of Indo-oceanic Mycobacterium tuberculosis (Mtb) strains leading to the loss of sulfolipid from these strains. By X-ray crystallographic analysis and molecular dynamics (MD) simulations, we show the importance of this residue in the global PapA2 structure. The presence of a Zn atom has not been reported before for this class of proteins. Here, we provide an important link between genomic alteration and its molecular consequence in Mtb highlighting one of the many adaptive mechanisms that have contributed to its success as a human pathogen. A high degree of identity with PapA1, 3, or 4 would help in interpreting the structure of these PapA proteins and other acyl transferases of other biological systems.

Evaluation of Antimicrobial and Antifungal efficacy of Chitosan as endodontic irrigant against Enterococcus Faecalis and Candida Albicans Biofilm formed on tooth substrate.

BACKGROUND: Bacterial biofilms formed on the root canal wall are often difficult to remove. This study aimed to evaluate the cytotoxic effect and antibacterial efficacy of chitosan when used as root canal irrigant against E. Faecalis and Candida albicans biofilm formed on tooth substrate. MATERIAL AND METHODS: The present study evaluated antibacterial effect of 0.25% Chitosan, 0.5% Chitosan, 2% chlorhexidine and 3% sodium hypochlorite against Enterococcus faecalis and Candida Albicans. Agar-well diffusion methods, minimal inhibitory concentration tests and biofilm susceptibility assays were used to determine antibacterial activity. Teeth specimens were sectioned to obtain a standardized tooth length of 12mm. Specimens were inoculated with 10 mL of the freshly prepared E. Faecalis suspension and Candida albicans for 4 weeks. The specimens were then instrumented with ProTaper rotary files F3 size. After irrigation with test solution, three sterile paper points were placed into one canal, left for 60 s and transferred to a test tube containing 1 mL of reduced transport fluid. The number of CFU in 1 mL was determined. RESULTS: 3-week biofilm qualitative assay showed complete inhibition of bacterial growth with 3% Sodium hypochlorite, 2% Chlorhexidine and Chitosan except saline, which showed presence of bacterial growth. Significant reduction of colony forming units (CFU)/mL was observed for the chitosan groups and the antibacterial activity of the chitosan groups was at par with 3% NaOCl and 2% Chlorhexidine. It was observed that the chitosan showed no cytotoxicity at 3mg/ml and 10% cytotoxicity at 6mg/ml. CONCLUSIONS: The use of chitosan as a root canal irrigant might be an alternative considering the various undesirable properties of NaOCl and chlorhexidine. Key words:Biofilm, Candida albicans, Chitosan, Cytotoxicity, Enterococcus faecalis.

Inhibition of Mycobacterium tuberculosis dihydrodipicolinate synthase by alpha-ketopimelic acid and its other structural analogues.

The Mycobacterium tuberculosis dihydrodipicolinate synthase (Mtb-dapA) is an essential gene. Mtb-DapA catalyzes the aldol condensation between pyruvate and L-aspartate-beta-semialdehyde (ASA) to yield dihydrodipicolinate. In this work we tested the inhibitory effects of structural analogues of pyruvate on recombinant Mtb-DapA (Mtb-rDapA) using a coupled assay with recombinant dihydrodipicolinate reductase (Mtb-rDapB). Alpha-ketopimelic acid (α-KPA) showed maximum inhibition of 88% and IC50 of 21 µM in the presence of pyruvate (500 µM) and ASA (400 µM). Competition experiments with pyruvate and ASA revealed competition of α-KPA with pyruvate. Liquid chromatography-mass spectrometry (LC-MS) data with multiple reaction monitoring (MRM) showed that the relative abundance peak of final product, 2,3,4,5-tetrahydrodipicolinate, was decreased by 50%. Thermal shift assays showed 1 °C Tm shift of Mtb-rDapA upon binding α-KPA. The 2.4 Å crystal structure of Mtb-rDapA-α-KPA complex showed the interaction of critical residues at the active site with α-KPA. Molecular dynamics simulations over 500 ns of pyruvate docked to Mtb-DapA and of α-KPA-bound Mtb-rDapA revealed formation of hydrogen bonds with pyruvate throughout in contrast to α-KPA. Molecular descriptors analysis showed that ligands with polar surface area of 91.7 Å(2) are likely inhibitors. In summary, α-hydroxypimelic acid and other analogues could be explored further as inhibitors of Mtb-DapA.

Small-Scale Screening to Large-Scale Over-Expression of Human Membrane Proteins for Structural Studies.

Membrane protein structural studies are frequently hampered by poor expression. The low natural abundance of these proteins implies a need for utilizing different heterologous expression systems. E. coli and yeast are commonly used expression systems due to rapid cell growth at high cell density, economical production, and ease of manipulation. Here we report a simplified, systematically developed robust strategy from small-scale screening to large-scale over-expression of human integral membrane proteins in the mammalian expression system for structural studies. This methodology streamlines small-scale screening of several different constructs utilizing fluorescence size-exclusion chromatography (FSEC) towards optimization of buffer, additives, and detergents for achieving stability and homogeneity. This is followed by the generation of stable clonal cell lines expressing desired constructs, and lastly large-scale expression for crystallization. These techniques are designed to rapidly advance the structural studies of eukaryotic integral membrane proteins including that of human membrane proteins.

Unsaturated Lipid Assimilation by Mycobacteria Requires Auxiliary cis-trans Enoyl CoA Isomerase.

Mycobacterium tuberculosis (Mtb) can survive in hypoxic necrotic tissue by assimilating energy from host-derived fatty acids. While the expanded repertoire of ß-oxidation auxiliary enzymes is considered crucial for Mtb adaptability, delineating their functional relevance has been challenging. Here, we show that the Mtb fatty acid degradation (FadAB) complex cannot selectively break down cis fatty acyl substrates. We demonstrate that the stereoselective binding of fatty acyl substrates in the Mtb FadB pocket is due to the steric hindrance from Phe287 residue. By developing a functional screen, we classify the family of Mtb Ech proteins as monofunctional or bifunctional enzymes, three of which complement the FadAB complex to degrade cis fatty acids. Crystal structure determination of two cis-trans enoyl coenzyme A (CoA) isomerases reveals distinct placement of active-site residue in Ech enzymes. Our studies thus reveal versatility of Mtb lipid-remodeling enzymes and identify an essential role of stand-alone cis-trans enoyl CoA isomerases in mycobacterial biology.

The role of cone beam computed tomography in the endodontic management of a mandibular first molar with three distal canals.

The presence of three root canals in the distal root of the mandibular first permanent molars is rare; based on in vitro studies its incidence is reported to be between 0.2% and 3%. With the advent of cone beam computed tomography (CBCT) as an adjunctive diagnostic aid, the determination of root canal anatomy in teeth with extra canals and complex canal configurations has become more precise. CBCT provides three dimensional visualization of the pulp canal space, allowing the clinician in determining the spatial relationships of the root canals with each other at various cross sectional levels along the length of the root. The present report discusses the endodontic management of a mandibular first permanent molar with three canals in the distal root, employing CBCT as an adjunctive diagnostic aid to conventional radiography.

Endodontic management of open apex using Biodentine as a novel apical matrix.

AIM: Endodontic management of open apex using Biodentine as an apical matrix. Summary : An immature tooth with pulpal necrosis and periapical pathology imposes a great difficulty to the endodontist. Endodontic treatment options for such teeth consist of conventional apexification procedure with and without apical barriers. Biodentine™ is new calcium silicate based cement that exhibits physical and chemical properties similar to those described for certain Portland cement derivatives. This article demonstrates the use of the newer material, Biodentine as an apical matrix barrier in root end apexification procedure. This case reports present apexification and successful healing with the use of Biodentine as an apical barrier matrix. Conclusion : Apexification in one step using an apical plug of Biodentine can be considered a predictable treatment and may be an alternative to mineral trioxide aggregate apexification.

Type III talon cusp and Type III B dens invaginatus occurring simultaneously in a mandibular lateral incisor.

Talon cusp and dens invaginatus are developmental anomalies of the human dentition. They not only affect the esthetic appearance of teeth but also may create difficulties during dental treatment and lead to a number of dental problems. Both anomalies are observed most commonly in the lateral maxillary incisor and rarely in the mandibular dentition. The simultaneous occurrence of talon cusp and dens invaginatus in a single tooth is very rare in the mandibular dentition and, to the authors' knowledge, has not yet been reported in a mandibular lateral incisor. This article presents a rare case of dens invaginatus and talon cusp occurring concurrently in a mandibular lateral incisor. Three-dimensional imaging modality was used to describe the complex internal anatomy.

General qPCR and Plate Reader Methods for Rapid Optimization of Membrane Protein Purification and Crystallization Using Thermostability Assays.

This unit describes rapid and generally applicable methods to identify conditions that stabilize membrane proteins using temperature-based denaturation measurements as a proxy for target time-dependent stability. Recent developments with thiol-reactive dyes sensitive to the unmasking of cysteine residues upon protein unfolding have allowed for routine application of thermostability assays to systematically evaluate the stability of membrane protein preparations after various purification procedures. Test conditions can include different lipid cocktails, lipid-detergent micelles, pH, salts, osmolytes, and potential active-site ligands. Identification and use of conditions that stabilize the structure have proven successful in enabling the structure determination of numerous families of membrane proteins that otherwise were intractable.

Successful management of pulpo-periodontal lesion in maxillary lateral incisor with palatogingival groove using CBCT scan.

Palatogingival groove is a rare developmental anomaly involving the lingual surface of the maxillary incisor and resulting in severe endodontic and periodontal lesions. This case report describes a multidisciplinary approach for the combined management of the endodontic and periodontal problems for successful rehabilitation of the involved tooth. Cone-beam computed tomography (CBCT) helped in correct diagnosis of the lesion and hence enabled effective treatment.

Exome sequencing and advances in crop improvement.

Next-generation sequencing strategies have opened new vistas for molecular plant breeding. The sequence information obtained by the advent of next-generation sequencing provides a valuable tool not only for improving domesticated crops but also for investigating the natural evolution of crops. Such information provides an enormous potential for sustainable agriculture. In this review, we discuss how such sequencing approaches have transformed exome sequencing into a practical utility that has enormous potential for crop improvement in agriculture. Furthermore, we also describe the future of crop improvement beyond the exome sequencing strategies.

Overexpressing human membrane proteins in stably transfected and clonal human embryonic kidney 293S cells.

X-ray crystal structures of human membrane proteins, although potentially of extremely great impact, are highly underrepresented relative to those of prokaryotic membrane proteins. One key reason for this is that human membrane proteins can be difficult to express at a level, and at a quality, suitable for structural studies. This protocol describes the methods that we use to overexpress human membrane proteins from clonal human embryonic kidney 293 (HEK293S) cells lacking N-acetylglucosaminyltransferase I (GnTI(-)), and was recently used in our 2.1-ŠX-ray crystal structure determination of human RhCG. Upon identification of highly expressing cell lines, suspension cell cultures are scaled up in a facile manner either using spinner flasks or cellbag bioreactors, resulting in a final purified yield of ∼0.5 mg of membrane protein per liter of medium. The protocol described here is reliable and cost effective, can be used to express proteins that would otherwise be toxic to mammalian cells and can be completed in 8-10 weeks.