Paricalcitol attenuates oxidative stress and inflammatory response in the liver of NAFLD rats by regulating FOXO3a and NFκB acetylation.

The lack of therapeutics along with complex pathophysiology made non-alcoholic fatty liver disease (NAFLD) a research hotspot. Studies showed that the deficiency of Vitamin D plays a vital role in NAFLD pathogenesis. While several research studies focused on vitamin D supplementation in NAFLD, there is still a need to understand the regulatory mechanism of direct vitamin D receptor activation in NAFLD. In the present study, we explored the role of direct Vitamin D receptor activation using paricalcitol in choline-deficient high-fat diet-induced NAFLD rat liver and its modulation on protein acetylation. Our results showed that paricalcitol administration significantly reduced the fat accumulation in HepG2 cells and the liver of NAFLD rats. Paricalcitol attenuated the elevated serum level of alanine transaminase, aspartate transaminase, insulin, low-density lipoprotein, triglyceride, and increased high-density lipoprotein in NAFLD rats. Paricalcitol significantly decreased the increased total protein acetylation by enhancing the SIRT1 and SIRT3 expression in NAFLD liver. Further, the study revealed that paricalcitol reduced the acetylation of NFκB and FOXO3a in NAFLD liver along with a decrease in the mRNA expression of IL1ß, NFκB, TNFα, and increased catalase and MnSOD. Moreover, total antioxidant activity, glutathione, and catalase were also elevated, whereas lipid peroxidation, myeloperoxidase, and reactive oxygen species levels were significantly decreased in the liver of NAFLD after paricalcitol administration. The study concludes that the downregulation of SIRT1 and SIRT3 in NAFLD liver was associated with an increased acetylated NFκB and FOXO3a. Paricalcitol effectively reversed hepatic inflammation and oxidative stress in NAFLD rats through transcriptional regulation of NFκB and FOXO3a, respectively, by inhibiting their acetylation.

Dengue dynamics: Prognostic and disease monitoring through molecular and serological profiling of clinical isolates.

BACKGROUND OBJECTIVES: Dengue fever is a mosquito-borne illness that affects millions of people worldwide every year. With no vaccination available, early detection and treatment is critical. One-hundred-twelve countries in the world pose a risk to travelers, particularly in metropolitan areas. Laboratory diagnoses vary according to objectives, resources, and schedule, with sensitivity and specificity must be balanced for effective testing. METHODS: The current work is a cross-sectional diagnostic study and samples from suspected patients of dengue was collected from May 15 to November 15 2023 and transported to laboratory, and RT-PCR and Dengue Duo Rapid test diagnosis techniques were used on 48 clinical samples included in this study. RESULTS: Blood was collected from suspected cases of dengue and subjected further to different molecular and serological parameters. Serum was separated from all 48 blood samples. RNA was isolated by silica column extraction method which is further utilized as a template for amplification and detection of dengue serotyping. Master Mix was prepared for the amplification and detection of dengue virus by Rotor-Gene Q Real-Time PCR Machine and further serological profiling of positive dengue cases was studied by conventional PCR. INTERPRETATION CONCLUSION: Our laboratory effectively standardized an RT-PCR-based approach for molecular identification of dengue virus in clinical specimens. This adaptive technique which used numerous primer sets displayed good specificity and sensitivity in serotype detection. The technology provides for quick and reliable identification of dengue virus infections, allowing for targeted treatment and preventative actions for successful disease management in highly populated regions.

Doxorubicin induces phosphorylation of lamin A/C and loss of nuclear membrane integrity: A novel mechanism of cardiotoxicity.

Lamin A/C, essential inner nuclear membrane proteins, have been linked to progeria, a disease of accelerated aging, and many other diseases, which include cardiac disorder. Lamin A/C mutation and its phosphorylation are associated with altering nuclear shape and size. The role of lamin A/C in regulating normal cardiac function was reported earlier. In the present study, we hypothesized that Doxorubicin (Dox) may alter total lamin A/C expression and phosphorylation, thereby taking part in cardiac injury. An in vitro cellular injury model was generated with Dox (0.1-10.0 µM) treatment on cardiomyoblast cells (H9c2) to prove our hypothesis. Increased size and irregular (ameboid) nucleus shape were observed in H9c2 cells after Dox treatment. Similarly, we have observed a significant increase in cell death on increasing the Dox concentration. The expression of lamin A/C and its phosphorylation at serine 22 significantly decreased and increased, respectively in H9c2 cells and rat hearts after Dox exposure. Phosphorylation led to depolymerization of the lamin A/C in the inner nuclear membrane and was evidenced by their presence throughout the nucleoplasm as observed by immunocytochemistry techniques. Thinning and perforation on the walls of the nuclear membrane were observed in Dox-treated H9c2 cells. LMNA-overexpression in H9c2 protected the cells from Dox-induced cell death, reversing all changes described above. Further, improvement of lamin A/C levels was observed in Dox-treated H9c2 cells when treated with Purvalanol A, a CDK1 inhibitor and N-acetylcysteine, an antioxidant. The study provides new insight regarding Dox-induced cardiac injury with the involvement of lamin A/C and alteration of inner nuclear membrane structure.

The structure and function of lamin A/C: Special focus on cardiomyopathy and therapeutic interventions.

Lamins are inner nuclear membrane proteins that belong to the intermediate filament family. Lamin A/C lie adjacent to the heterochromatin structure in polymer form, providing skeletal to the nucleus. Based on the localization, lamin A/C provides nuclear stability and cytoskeleton to the nucleus and modulates chromatin organization and gene expression. Besides being the structural protein making the inner nuclear membrane in polymer form, lamin A/C functions as a signalling molecule involved in gene expression as an enhancer inside the nucleus. Lamin A/C regulates various cellular pathways like autophagy and energy balance in the cytoplasm. Its expression is highly variable in differentiated tissues, higher in hard tissues like bone and muscle cells, and lower in soft tissues like the liver and brain. In muscle cells, including the heart, lamin A/C must be expressed in a balanced state. Lamin A/C mutation is linked with various diseases, such as muscular dystrophy, lipodystrophy, and cardiomyopathies. It has been observed that a good number of mutations in the LMNA gene impact cardiac activity and its function. Although several works have been published, there are still several unexplored areas left regarding the lamin A/C function and structure in the cardiovascular system and its pathological state. In this review, we focus on the structural organization, expression pattern, and function of lamin A/C, its interacting partners, and the pathophysiology associated with mutations in the lamin A/C gene, with special emphasis on cardiovascular diseases. With the recent finding on lamin A/C, we have summarized the possible therapeutic interventions to treat cardiovascular symptoms and reverse the molecular changes.

Electrostatic-Driven Self-Assembly of Janus-like Monolayer-Protected Metal Nanoclusters.

The generation of controlled microstructures of functionalized nanoparticles has been a crucial challenge in nanoscience and nanotechnology. Efforts have been made to tune ligand charge states that can affect the aggregation propensity and modulate the self-assembled structures. In this work, we modeled zwitterionic Janus-like monolayer ligand-protected metal nanoclusters (J-MPCs) and studied their self-assembly using atomistic molecular dynamics and on-the-fly probability-based enhanced sampling simulations. The oppositely charged ligand functionalization on two hemispheres of a J-MPC elicits asymmetric solvation, primarily driven by distinctive hydrogen bonding patterns in the ligand-solvent interactions. Electrostatic interactions between the oppositely charged residues in J-MPCs guide the formation of one-dimensional and ring-like self-assembled superstructures with molecular dipoles oriented in specific patterns. The pertinent atomistic insights into the intermolecular interactions governing the self-assembled structures of zwitterionic J-MPCs obtained from this work can be used to design a general strategy to create tunable microstructures of charged MPCs.

Effect of neuronavigated repetitive Transcranial Magnetic Stimulation on pain, cognition and cortical excitability in fibromyalgia syndrome.

BACKGROUND: Fibromyalgia syndrome is a widespread chronic pain condition identified by body-wide pain, fatigue, cognitive fogginess, and sleep issues. In the past decade, repetitive transcranial magnetic stimulation has emerged as a potential management tool.. In the present study, we enquired whether repetitive transcranial magnetic stimulation could modify pain, corticomotor excitability, cognition, and sleep. METHODS: Study is a randomized, sham-controlled, double-blind, clinical trial; wherein after randomizing thirty-four fibromyalgia patients into active or sham therapy (n = 17 each), each participant received repetitive transcranial magnetic stimulation therapy. In active therapy was given at 1 Hz for 20 sessions were delivered on dorsolateral prefrontal cortex (1200 pulses, 150 pulses per train for 8 trains); while in sham therapy coil was placed at right angle to the scalp with same frequency. Functional magnetic resonance imaging was used to identify the therapeutic site. Pain intensity, corticomotor excitability, cognition, and sleep were examined before and after therapy. RESULTS: Baseline demographic and clinical parameters for both active and sham groups were comparable. In comparison to sham, active repetitive transcranial magnetic stimulation showed significant difference in pain intensity (P < 0.001, effect size = 0.29, large effect) after intervention. Other parameters of pain perception, cognition, and sleep quality also showed a significant improvement after the therapy in active therapy group only, as compared to sham. CONCLUSIONS: Findings suggest that repetitive transcranial magnetic stimulation intervention is effective in managing pain alongside cognition and sleep disturbances in patients of fibromyalgia. It may prove to be an important tool in relieving fibromyalgia-associated morbidity.

Insights into the Interactions of Peptides with Monolayer-Protected Metal Nanoclusters.

Monolayer-protected atomically precise metal nanoclusters (MPCs) have potential applications in catalysis, imaging, and drug delivery. Understanding their interactions with biomolecules such as peptides is of paramount interest for their use in cell imaging and drug delivery. Here we have carried out atomistic molecular dynamics simulations to investigate the interactions between MPCs and an anticancer peptide, melittin. Melittin gets attached to the MPCs surface by the formation of multiple hydrogen bonds between its amino acid residues with MPCs ligands. Additionally, the positively charged Lys, Arg, and peptide's N-terminal strongly anchor the peptide to the MPC metal surface, providing extra stabilization.

Exploring bixin from Bixa orellana L. seeds: quantification and in silico insights into its anti-cancer potential.

Bixin, the key pigment of Bixa orellana L., is an apo-carotenoid found in the seed arils. The present study aimed to quantitatively determine the bixin content of seeds and explore its anti-cancer activity through in silico studies. The bixin content from the seeds of the local genotype, TNMTP8, quantified by RP-HPLC was 4.58 mg per gram. The prediction of pharmacological activity suggested that bixin may serve as a BRAF, MMP9, TNF expression inhibitors, and TP53 expression enhancer. According to molecular docking analysis, bixin interacted with eight different skin cancer targets and had the lowest binding energy compared to the standard drug, 5-fluorouracil. The binding score between bixin and the targets ranged from -4.7 to -8.7 kcal/mol. The targets BRAF and SIRT3 interacted well with bixin, with binding energies as low as -8.3 and -8.7 kcal/mol, respectively. Hence, the dynamic behavior of these two docked complexes throughout a 500 ns trajectory run was investigated further. The Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF) values, and total contacts as a function of time recorded during scrutiny suggest that both complexes were stable. This was validated by post-molecular dynamics analysis using Molecular Mechanics Generalized Born Surface Area (MM-GBSA). Principal component analysis (PCA) was used to analyze the significant differences in motion exhibited by BRAF-Bixin and SIRT3-Bixin. The results showed that bixin is a promising source for potential treatment interventions in skin cancer therapies.Communicated by Ramaswamy H. Sarma.

Reduction of esters to alcohols and iodides using aminodiborane (µ-NH2B2H5): scope and mechanistic investigations.

Herein, we report an efficient methodology for the reduction of esters, carbonates, and anhydrides to alcohols using in situ generated aminodiborane from iodine and ammonia borane. This methodology also finds use for the transformation of esters to iodides by varying the stoichiometry of reagents. The protocol has broad substrate scope for transformation of esters to alcohols and iodides with excellent yields. The method is also useful for synthesizing pharmaceutically and industrially important compounds such as a Cinacalcet precursor, a Streptoindole analogue, and 1,4-pentanediol. Control studies and DFT calculations carried out to study the reduction mechanism of esters using aminodiborane indicate that a dioxaborinamine intermediate is formed during the reaction.

Understanding Molecular Aggregation of Ligand-Protected Atomically-Precise Metal Nanoclusters.

Monolayer-protected atomically precise nanoclusters (MPCs) are an important class of molecules due to their unique structural features and diverse applications, including bioimaging, sensors, and drug carriers. Understanding the atomistic and dynamical details of their self-assembly process is crucial for designing system-specific applications. Here, we applied molecular dynamics and on-the-fly probability-based enhanced sampling simulations to study the aggregation of Au25(pMBA)18 MPCs in aqueous and methanol solutions. The MPCs interact via both hydrogen bonds and π-stacks between the aromatic ligands to form stable dimers, oligomers, and crystals. The dimerization free energy profiles reveal a pivotal role of the ligand charged state and solvent mediating the molecular aggregation. Furthermore, MPCs' ligands exhibit suppressed conformational flexibility in the solid phase due to facile intercluster hydrogen bonds and π-stacks. Our work provides unprecedented molecular-level dynamical details of the aggregation process and conformational dynamics of MPCs ligands in solution and crystalline phases.

Structure modelling of odorant receptor from Aedes aegypti and identification of potential repellent molecules.

Odorant receptors (ORs) are important class of proteins involved in olfactory behaviour of insects. These are GPCR-like heptahelical transmembrane proteins with inverted topology compared to GPCR and require a co-receptor (ORco) for their function. OR function can be modulated through small molecules and negative modulation can be beneficial in case of disease vectors like Aedes aegypti. OR4 of A. aegypti is implicated in host recognition through human odour. Aedes aegypti is a vector for viruses that spread diseases like dengue, Zika and Chikungunya. In this study, we have attempted to model the full-length structure of OR4 and the ORco of A. aegypti due to lack of experimental structure. Further, we have screened a library of natural compounds (>0.3 million) along with known repellent molecules against ORco and OR4. Many natural compounds, including those from plants like Ocimum tenuiflorum (Holy Basil) and Piper nigrum (Black pepper), were found to have better binding affinity towards ORco compared to known repellents like DEET providing an alternative to existing repellent molecules. For specific inhibitor of OR4, several natural compounds (including those from plant like Mulberry) were identified. Further, we have utilized multiple docking approaches and conservation analysis to understand the interaction between OR4 and ORco. It was observed that the residues from the seventh transmembrane helix of OR4 and pore forming helix of ORco could play an important role along with known intracellular loop 3 residues in mediating the heteromer formation of OR and ORco.

Structural modelling and dynamics of full-length of TLR10 sheds light on possible modes of dimerization, ligand binding and mechanism of action.

Toll like receptors (TLRs) play a pivotal role in innate and adaptive immunity. There are 10 TLRs in the human genome, of which TLR10 is the least characterized. Genetic polymorphism of TLR10 has been shown to be associated with multiple diseases including tuberculosis and rheumatoid arthritis. TLR10 consists of an extracellular domain (ECD), a single-pass transmembrane (TM) helix and intracellular TIR (Toll/Interleukin-1 receptor) domain. ECD is employed for ligand recognition and the intracellular domain interacts with other TIR domain-containing adapter proteins for signal transduction. Experimental structure of ECD or TM domain is not available for TLR10. In this study, we have modelled multiple forms of TLR10-ECD dimers, such as closed and open forms, starting from available structures of homologues. Subsequently, multiple full-length TLR10 homodimer models were generated by utilizing homology modelling and protein-protein docking. The dynamics of these models in membrane-aqueous environment revealed the global motion of ECD and TIR domain towards membrane bilayer. The TIR domain residues exhibited high root mean square fluctuation compared to ECD. The 'closed form' model was observed to be energetically more favorable than 'open form' model. The evaluation of persistent interchain interactions, along with their conservation score, unveiled critical residues for each model. Further, the binding of dsRNA to TLR10 was modelled by defined and blind docking approaches. Differential binding of dsRNA to the protomers of TLR10 was observed upon simulation that could provide clues on ligand disassociation. Dynamic network analysis revealed that the 'open form' model can be the functional form while 'closed form' model can be the apo form of TLR10.

Collective Variables for Crystallization Simulations-from Early Developments to Recent Advances.

Crystallization is an important physicochemical process which has relevance in material science, biology, and the environment. Decades of experimental and theoretical efforts have been made to understand this fundamental symmetry-breaking transition. While experiments provide equilibrium structures and shapes of crystals, they are limited to unraveling how molecules aggregate to form crystal nuclei that subsequently transform into bulk crystals. Computer simulations, mainly molecular dynamics (MD), can provide such microscopic details during the early stage of a crystallization event. Crystallization is a rare event that takes place in time scales much longer than a typical equilibrium MD simulation can sample. This inadequate sampling of the MD method can be easily circumvented by the use of enhanced sampling (ES) simulations. In most of the ES methods, the fluctuations of a system's slow degrees of freedom, called collective variables (CVs), are enhanced by applying a bias potential. This transforms the system from one state to the other within a short time scale. The most crucial part of such CV-based ES methods is to find suitable CVs, which often needs intuition and several trial-and-error optimization steps. Over the years, a plethora of CVs has been developed and applied in the study of crystallization. In this review, we provide a brief overview of CVs that have been developed and used in ES simulations to study crystallization from melt or solution. These CVs can be categorized mainly into four types: (i) spherical particle-based, (ii) molecular template-based, (iii) physical property-based, and (iv) CVs obtained from dimensionality reduction techniques. We present the context-based evolution of CVs, discuss the current challenges, and propose future directions to further develop effective CVs for the study of crystallization of complex systems.

A dimer between monomers and hexamers-Oligomeric variations in glucosamine-6-phosphate deaminase family.

In bacteria that live in hosts whose terminal sugar is a sialic acid, Glucosamine-6-phosphate deaminase (NagB) catalyzes the last step in converting sialic acid into Fructose-6-phosphate. These bacteria then use the Fructose-6-phosphate as an energy source. The enzyme NagB exists as a hexamer in Gram-negative bacteria and is allosterically regulated. In Gram-positive bacteria, it exists as a monomer and lacks allosteric regulation. Our identification of a dimeric Gram-negative bacterial NagB motivated us to characterize the structural basis of two closely related oligomeric forms. We report here the crystal structures of NagB from two Gram-negative pathogens, Haemophilus influenzae (Hi) and Pasturella multocida (Pm). The Hi-NagB is active as a hexamer, while Pm-NagB is active as a dimer. Both Hi-NagB and Pm-NagB contain the C-terminal helix implicated as essential for hexamer formation. The hexamer is described as a dimer of trimers. In the Pm-NagB dimer, the dimeric interface is conserved. The conservation of the dimer interface suggests that the three possible oligomeric forms of NagB are a monomer, a dimer, and a trimer of dimers. Computational modeling and MD simulations indicate that the residues at the trimeric interface have less stabilizing energy of oligomer formation than those in the dimer interface. We propose that Pm-NagB is the evolutionary link between the monomer and the hexamer forms.

Cooperative Friedel-Crafts Alkylation of Electron-Deficient Arenes via Catalyst Activation with Hexafluoroisopropanol.

A Friedel-Crafts alkylation of electron-deficient arenes with aldehydes through ''catalyst activation'' is presented. Through hydrogen bonding interactions, the solvent 1,1,1,3,3,3, -hexafluoroisopropanol (HFIP) interacted with the added Brønsted acid catalyst pTSA•H2 O, increasing its acidity. This activated catalyst enabled the Friedel-Crafts alkylation of electron-neutral as well as electron-deficient arenes. Strongly electron withdrawing arenes including arenes with multiple halogen atoms, NO2 , CHO, CO2 R, and CN, groups acted as efficient nucleophiles in this reaction. DFT studies reveal multiple roles of solvent HFIP viz; increasing the Brønsted acidity of the catalyst pTSA•H2 O, and stabilization of the transition states through a concerted pathway enabling the challenging reaction.

Therapeutic Potential of HDAC Inhibitors in the Treatment of Cardiac Diseases: A Short Review.

Protein acetylation is a reversible central mechanism to control gene expression and cell signaling events. Current evidence suggests that pharmacological inhibitors for protein deacetylation have already been used in various disease conditions. Accumulating reports showed that several compounds that enhance histone acetylation in cells are in both the preclinical and clinical development stages targeting non-communicable diseases, which include cancerous and non-cancerous especially cardiovascular complications. These compounds are, in general, enzyme inhibitors and target a family of enzymes- called histone deacetylases (HDACs). Since HDAC inhibitors have shown to be helpful in preclinical models of cardiac complications, further research on developing novel compounds with high efficacy and low toxicity may be essential for treating cardiovascular diseases. In this review, we have highlighted the roles of HDAC and its inhibitors in cardiac complications.

Understanding cyclic(alkyl)(amino)carbene-copper complex catalysed N-H and O-H bond addition to electron deficient olefins.

The hydroamination of electron-deficient olefins was carried out using the (CAAC)Cu-Cl (CAAC = cyclic (alkyl)(amino)carbene) catalyst with an excellent yield at room temperature and under an open atmosphere. Furthermore, the catalyst shows excellent efficiency in the hydroaryloxylation and hydroalkoxylation of alkenes under mild conditions. The efficiency of the catalyst was tested for a wide range of substrates with different electronic and steric functionalities. Detailed computational studies have been carried out to understand the mechanism of these Cu(I) catalyzed reactions, which revealed that the reaction proceeds via either a four-membered or a six-membered cyclic transition state containing the copper ion.

Pregestational diabetes alters cardiac structure and function of neonatal rats through developmental plasticity.

Pregestational diabetes (PGDM) leads to developmental impairment, especially cardiac dysfunction, in their offspring. The hyperglycemic microenvironment inside the uterus alters the cardiac plasticity characterized by electrical and structural remodeling of the heart. The altered expression of several transcription factors due to hyperglycemia during fetal development might be responsible for molecular defects and phenotypic changes in the heart. The molecular mechanism of the developmental defects in the heart due to PGDM remains unclear. To understand the molecular defects in the 2-days old neonatal rats, streptozotocin-induced diabetic female rats were bred with healthy male rats. We collected 2-day-old hearts from the neonates and identified the molecular basis for phenotypic changes. Neonates from diabetic mothers showed altered electrocardiography and echocardiography parameters. Transcriptomic profiling of the RNA-seq data revealed that several altered genes were associated with heart development, myocardial fibrosis, cardiac conduction, and cell proliferation. Histopathology data showed the presence of focal cardiac fibrosis and increased cell proliferation in neonates from diabetic mothers. Thus, our results provide a comprehensive map of the cellular events and molecular pathways perturbed in the neonatal heart during PGDM. All of the molecular and structural changes lead to developmental plasticity in neonatal rat hearts and develop cardiac anomalies in their early life.

Identification of potential modulators of IFITM3 by in-silico modeling and virtual screening.

IFITM3 is a transmembrane protein that confers innate immunity. It has been established to restrict entry of multiple viruses. Overexpression of IFITM3 has been shown to be associated with multiple cancers, implying IFITM3 to be good therapeutic target. The regulation of IFITM3 activity is mediated by multiple post-translational modifications (PTM). In this study, we have modelled the structure of IFITM3, consistent with experimental predictions on its membrane topology. MD simulation in membrane-aqueous environment revealed the stability of the model. Ligand binding sites on the IFITM3 surface were predicted and it was observed that the best site includes important residues involved in PTM and has good druggable score. Molecular docking was performed using FDA approved ligands and natural ligands from Super Natural II database. The ligands were re-ranked by calculating binding free energy. Select docking complexes were simulated again to substantiate the binding between ligand and IFITM3. We observed that known drugs like Eluxadoline and natural products like SN00224572 and Parishin A have good binding affinity against IFITM3. These ligands form persistent interactions with key lysine residues (Lys83, Lys104) and hence can potentially alter the activity of IFITM3. The results of this computational study can provide a starting point for experimental investigations on IFITM3 modulators.

A Catalyst and Solvent Free Route for the Synthesis of N-Substituted Pyrrolidones from Levulinic Acid.

An efficient, metal-free, catalyst-free and solvent-free methodology for the reductive amination of levulinic acid with different anilines has been developed using HBpin as the reducing reagent. This protocol offers an excellent method to avoid solvents and added catalysts on the synthesis of different kinds of N-substituted pyrrolidones under metal free conditions. It is also the first report for the synthesis of different pyrrolidones by solvent-free as well as catalyst-free methods. The proposed mechanism for the formation of pyrrolidone has been supported by DFT calculations and control experiments.