Nanocarriers for the Delivery of Quercetin to Inhibit the UV-Induced Aggregation of γD-Crystallin

Due to gradual environmental changes like ozone layer depletion and global warming, human eyes are exposed to UV light. Exposure to UV light can be a cause of cataracts, one of the ocular diseases that may cause vision impairment. To date, lens replacement has been the only treatment available for cataracts. In our present study, we carried out an extensive examination of polyphenols as inhibitors for UV-induced aggregation of γD-crystallin. On exposure to UV-C light, γD-crystallin forms fibrils instead of amorphous aggregates. Various polyphenols were tested as inhibitors; out of them, quercetin, baicalein, and caffeic acid were found to be effective. As polyphenols are insoluble in water, nanoencapsulation was used to enhance their bioavailability. CS-TPP and CS-PLGA encapsulating systems were considered, as they form biodegradable nanocapsules. Out of three polyphenols (quercetin, baicalein, and caffeic acid), quercetin forms nanocarriers of smaller sizes, a must for crossing the retinal barrier. Quercetin nanocarriers were considered an effective system that could be used for therapeutic applications. For these nanocarriers, encapsulation efficiency and polyphenol release kinetics were studied. CS-PLGA NPs were found to have a better loading efficiency for quercetin than CS-TPP NPs.

The minimum effective dose (ED90) of prophylactic oxytocin infusion during cesarean delivery in patients with and without obesity: an up-down sequential allocation dose-response study

BACKGROUND

Obesity is associated with greater oxytocin requirement during labor induction or augmentation. There are scant data exploring the intra-operative requirement during cesarean delivery in patients with obesity, and none comparing it with those without obesity. We evaluated the minimum effective dose (ED90) of an oxytocin infusion to achieve adequate uterine tone during cesarean delivery in patients with and without obesity.

METHODS

Patients (body mass index ≥30 kg/m2 represented patients with obesity) undergoing cesarean delivery using subarachnoid block were included. This prospective dual-arm dose-finding study used a 9:1 biased sequential allocation design. Oxytocin infusion was initiated at 13 IU/h at cord clamping in the first patient of each group. Uterine tone was graded as satisfactory or unsatisfactory by the obstetrician four minutes after initiation of the infusion. The dose of oxytocin infusion for subsequent patients was determined according to the response of the previous patient in the group. Oxytocin-associated side effects were evaluated. Dose-response data for the groups was evaluated using log-logistic function and ED90 estimates derived from fitted equations using the delta method.

RESULTS

The ED90 of oxytocin was significantly higher for patients with obesity (n = 40) compared with those without obesity (n = 40) [25.7 IU/h, 95% CI 18.6 to 32.9) vs. 16.6 IU/h, 95% CI 14.9 to 18.3)]; relative ratio 1.55 [95% CI 1.09 to 2.01] (P = 0.019).

CONCLUSIONS

Patients with obesity require a higher intra-operative oxytocin infusion dose rate to achieve a satisfactorily contracted uterus after fetal delivery when compared with patients without obesity.

Binding studies of potential amyloid-β inhibiting chalcone derivative with bovine serum albumin

Chalcones (α-phenyl-β-benzoylethylene) and their natural-source derivatives have been investigated for their remarkable biological activities, like neuroprotective, anti-inflammatory, and anti-tumor properties. A triazole chalcone ligand (E)-3-(4-(dimethylamino)phenyl)-1-(4-((1-(2-(4-((E)-3-(4(dimethylamino)phenyl)acryloyl)phenoxy)ethyl)-1H-1,2,3-triazol-4-yl)methoxy)phenyl)prop-2-en-1-one (L1) was synthesized by Cu(I)- catalysed click reaction. The mechanistic properties of L1 for therapy were evaluated by analyzing the binding interactions between L1 and bovine serum albumin (BSA) through photophysical and computational studies. The structural elucidation of ligand L1 was carried out by NMR and mass spectrometry. The Aβ inhibitory activity of L1 was studied by thioflavin T assay and transmission electron microscopy. The biomolecular interaction of L1 with bovine serum albumin was examined through multi-spectroscopic techniques in combination with in silico studies. UV-Visible absorption, fluorescence spectroscopy, circular dichroism, Förster resonance energy transfer, and three-dimensional fluorescence studies confirmed the formation of a BSA-L1 complex. The potential binding sites, mechanism of interactions, and variations in the environment of tyrosine and tryptophan amino acid residues of BSA were assessed at different temperatures. The binding constant for the Static quenching mechanism of intrinsic fluorescence of BSA was of the order of 105 M-1. The esterase enzyme activity assay in the presence of L1 revealed an increase in the protein enzyme activity. Molecular docking studies suggested L1 was predominantly bound to BSA by hydrogen bonds and Van der Waals forces.

Rational design and synthesis of novel triazole- and tetrazole-fused iminosugars as potential inhibitors of amyotrophic lateral sclerosis (ALS) linked SOD1 aggregation

In this manuscript we report the first example of an iminosugar that inhibits superoxide dismutase fibrillation associated with the amyotrophic lateral sclerosis (ALS). The present work involves synthesis of novel triazole and tetrazole embedded iminosugars, synthesized in 11-13 high yielding steps starting from readily available tri-O-benzyl-D-glucal and proceeding through a concomitant azidation - thermal intramolecular [3 + 2] cycloaddition reaction as the key step. One of these pre-designed iminosugars was found to inhibit fibrillation of SOD1 and also has shown propensity to break pre-formed fibrils. Docking and MD simulation studies suggest that the most probable interaction of this compound is a hydrogen bonding with Arg69, a loop IV residue of SOD1, which has a crucial role in stabilizing the native conformation of SOD1.

Effect of flavonoids on the destabilization of α-synuclein fibrils and their conversion to amorphous aggregate: A molecular dynamics simulation and experimental study

The second most prevalent neurodegenerative disease, Parkinson's disease (PD), is caused by the accumulation and deposition of fibrillar aggregates of the α-Syn into the Lewy bodies. To create a potent pharmacological candidate to destabilize the preformed α-Syn fibril, it is important to understand the precise molecular mechanism underlying the destabilization of the α-Syn fibril. Through molecular dynamics simulations and experiments, we have examined the molecular mechanisms causing the destabilization and suppression of a newly discovered α-Syn fibril with a Greek-key-like shape and an aggregation prone state (APS) of α-Syn in the presence and absence of various Flvs. According to MD simulation and experimental evidence, morin, quercetin, and myricetin are the Flvs, most capable of destabilizing the fibrils and converting them into amorphous aggregates. Compared to galangin and kaempferol, they have more hydroxyl groups and form more hydrogen bonds with fibrils.The processes by which morin and myricetin prevent new fibril production from APS and destabilize the fibrils are different. According to linear interaction energy analysis, van der Waals interaction predominates with morin, and electrostatic interaction dominates with myricetin. Our MD simulation and experimental findings provide mechanistic insights into how Flvs destabilize α-Syn fibrils and change their morphology, opening the door to developing structure-based drugs for treating Parkinson's disease.

Screening of Multitarget-Directed Natural Compounds as Drug Candidates for Alzheimer's Disease Using In Silico Techniques: Their Extraction and In Vitro Validation

Alzheimer's disease (AD) is a neurodegenerative disorder that impairs neurocognitive function. Acetylcholinesterase (AChE) and β-site APP cleaving enzyme 1 (BACE1) are the two main proteins implicated in AD. Indeed, the major available commercial drugs (donepezil, rivastigmine, and galantamine) against Alzheimer's are AChE inhibitors. However, none of these drugs are known to reverse or reduce the pathophysiological condition of the disease since there are multiple contributing factors to AD. Therefore, there is a need to develop a multitarget-directed ligand approach for its treatment. In the present study, plant bioactive compounds were screened for their AChE and BACE1 inhibition potential by conducting molecular docking studies. Considering their docking score and pharmacokinetic properties, limonin, peimisine, serratanine B, and withanolide A were selected as the lead compounds. Molecular dynamics simulations of these protein-ligand complexes confirmed the conformational and energetically stabilized enzyme-inhibitor complexes. The inhibition potential of the lead compounds was validated by in vitro enzyme assay. Withanolide A inhibited AChE (IC50 value of 107 μM) and showed mixed-type inhibition. At this concentration, it inhibited BACE1 activity by 57.10% and was stated as most effective. Both the compounds, as well as their crude extracts, were found to have no cytotoxic effect on the SH-SY5Y cell line.

Mechanism of the interaction of toxic SOD1 fibrils with two potent polyphenols: curcumin and quercetin

Amyotrophic lateral sclerosis (ALS) is a debilitating neurodegenerative disease commonly caused due to the aggregation of superoxide dismutase 1 (SOD1) protein. Finding inhibitors of SOD1 aggregation is of prime concern, but understanding the mechanistic action of inhibitors is equally important. Recent experiments found that two polyphenols, curcumin, and quercetin, have the ability to inhibit SOD1 aggregation. Quercetin was experimentally proven to break pre-formed fibrils into shorter segments, while curcumin did not significantly affect the pre-formed species. Here, we delve deeper into understanding the mechanism of action of quercetin and curcumin on pre-formed octameric fibrils of SOD1 (28PVKVWGSIKGL38: chains A-H) with the help of molecular dynamics (MD) simulations of a fibril docked polyphenol complex. Our results suggest that quercetin shows π-π stacking interaction with one of the key residues for toxic amyloid formation, Trp 32 of chains D, E, and F, and breaks the peptide chains G, and H from the rest of the fibril. On the other hand, curcumin binds to the hydrophobic amino acids of almost all the chains B-H and stabilizes the fibril rather than destabilizing it. Binding free energy calculations using MM/PBSA showed that curcumin binds more strongly to the SOD1 fibril due to greater van der Waals interactions compared to quercetin. These findings provide insights for the development of potential ALS treatments.

Myricetin: A Potent Anti-Amyloidogenic Polyphenol against Superoxide Dismutase 1 Aggregation

Amyotrophic lateral sclerosis (ALS) is believed to be caused by the aggregation of misfolded or mutated superoxide dismutase 1 (SOD1). As there is currently no treatment, research into aggregation inhibitors continues. Based on docking, molecular dynamics (MD) simulations, and experimental observations, we propose that myricetin, a plant flavonoid, can act as a potent anti-amyloidogenic polyphenol against SOD1 aggregation. Our MD simulation results showed that myricetin stabilizes the protein interface, destabilizes the preformed fibril, and decreases the rate of fibril elongation. Myricetin inhibits the aggregation of SOD1 in a dose-dependent manner as shown by the ThT aggregation kinetics curves. Our transmission electron microscopy, dynamic light scattering, and circular dichroism experiments indicate that fewer shorter fibrils have formed. Fluorescence spectroscopy results predict the involvement of a static quenching mechanism characterized by a strong binding between protein and myricetin. Importantly, size exclusion chromatography revealed the potential of myricetin for fibril destabilization and depolymerization. These experimental observations complement the MD results. Thus, myricetin is a potent SOD1 aggregation inhibitor that can reduce the fibril load. Using the structure of myricetin as a reference, it is possible to design more effective therapeutic inhibitors against ALS that prevent the disease and reverse its effects.

In silico study of interaction of (ZnO)12 nanocluster to glucose oxidase-FAD in absence and presence of glucose

Diabetes mellitus is one of the foremost global concerns, as it has impacted millions of lives. Therefore, there is an urgent need to develop a technology for continuous glucose monitoring in vivo. In the current study, we employed computational methods such as docking, MD simulations, and MM/GBSA, to obtain molecular insights into the interaction between (ZnO)12 nanocluster and glucose oxidase (GOx) that cannot be obtained through experiments alone. For this, theoretical modeling of the 3D cage-like (ZnO)12 nanocluster in ground state configuration was performed. Further docking of (ZnO)12 nanocluster with GOx molecule was carried out to find the nano-bio-interaction of (ZnO)12-GOx complex. To understand the whole interaction and dynamics of (ZnO)12-GOx-FAD-with and without glucose, we performed MD simulation and MM/GBSA analysis of (ZnO)12-GOx-FAD complex and glucose-(ZnO)12-GOx-FAD complex separately. The interaction was found to be stable, and the binding energy of (ZnO)12 to GOx-FAD increases in the presence of glucose by 6 kcal mol-1. This may be helpful in nano probing of the interaction of GOx with glucose. It can help in making a device like fluorescence resonance energy transfer (FRET) based nano-biosensor to monitor the glucose level in pre and post diabetic patient.Communicated by Ramaswamy H. Sarma.

A computational strategy for therapeutic development against superoxide dismutase (SOD1) amyloid formation: effect of polyphenols on the various events in the aggregation pathway

Pathology of superoxide dismutase 1 (SOD1) aggregation is linked to a neurodegenerative disease known as amyotrophic lateral sclerosis (ALS). Without suitable post-translational modifications (PTMs), the protein structure tends to become aggregation-prone. Understanding the role of PTMs and targeting the aggregation-prone SOD1 with small molecules can be used to design a strategy to inhibit its aggregation. Microsecond long molecular dynamics (MD) simulations followed by free energy surface (FES) analyses show that the loss of structure in the apo monomer happens locally and stepwise. Removing the disulfide bond from apoprotein leads to further instability in the zinc-binding loop, giving rise to non-native protein conformations. Further, it was found that these non-native conformations have a higher propensity to form a non-native dimer. We chose three structurally similar polyphenols based on their binding energies and investigated their impact on SOD1 aggregation kinetics. MD simulations of apo-SOD1^SH/corkscrew fibril-polyphenol complexes were also carried out. The effect of polyphenols was seen on fibril elongation as well. Based on the experiments and MD simulation results, it can be inferred that the choice of inhibitors is influenced not only by the binding energy but also by dimer interface stabilization, the proclivity to form non-native dimers, the propensity to break fibrils, and the propensity to decrease the rate of elongation. The polyphenols with 3' and 4' hydroxyl groups are better inhibitors of SOD1 aggregation.

Nano-Formulation of Antioxidants as Effective Inhibitors of γD-Crystallin Aggregation

The aggregation of crystallin proteins is related to cataracts and age-related macular degeneration. Apart from surgical replacement of the cataract lens, no other alternative treatment is available till date for this ailment. In the current work, we carried out an in-depth investigation of the effect of polyphenol-loaded nano-formulations on the aggregation of γD-crystallin. At first, the protein was allowed to form amorphous aggregates under denaturing conditions. Several polyphenols were then tried to inhibit the aggregation of the protein. Among the polyphenols tested, resveratrol and quercetin were found to be the most effective. Since polyphenols are prone to degradation, they were encapsulated in chitosan nanoparticles in order to provide ambient conditions for them to function effectively. The loading efficiency and polyphenol release kinetics were subsequently tested. Finally, the efficacy of resveratrol/quercetin-loaded chitosan nano-particles as inhibitors of γD-crystallin aggregation was confirmed in a series of experiments demonstrating the potency of the system in the prospective therapeutic intervention of eye ailments concerning self-assembly of γD-crystallin proteins.

Current advancement in the development of manganese complexes as magnetic resonance imaging probes

Emerging non-invasive molecular imaging modalities can detect a pathophysiological state at the molecular level before any anatomic changes are observed. Magnetic resonance imaging (MRI) is preferred over other nuclear imaging techniques owing to its radiation-free approach. Conventionally, most MRI contrast agents employed predominantly involve lanthanide metal: Gadolinium (Gd) until the discovery of associated severe nephrogenic toxicity issues. This limitation led a way to the development of manganese-based contrast agents which offer similar positive contrast enhancement capability. A vast quantity of experimental data has been accumulated over the last decade to define the physicochemical characteristics of manganese chelates with various ligand scaffolds. One can now observe how the ligand configurations, rigidity, and donor-acceptor characteristics impact the stability of the complex. This review covers the current trends in the development of manganese-based MRI contrast agents, the mechanisms they are based on and design considerations for newer manganese-based contrast agents with higher diagnostic strength along with better safety profiles.

Role of molecular and chemical chaperon in assisting refolding of BMP2 in E. coli

Bone morphogenetic protein 2 (BMP2) when expressed in bacteria forms inclusion bodies (IBs) due to its complex disulfide-rich structure. Chaperons are already well known for their role in assisting protein folding. In our studies, we have used two E. coli strains, BL21(DE3) and SHuffle® T7 cells for overexpressing BMP2 in soluble fraction. We observed that SHuffle® T7 cells successfully expressed soluble functionally active BMP2 in presence of molecular and chemical chaperones at low temperature. The combination of chemical and molecular chaperons further increases the yield of protein. The best-suited chaperon system for overexpression of BMP2 is GroES-GroEL at low temperature. The soluble functionally active BMP2 is confirmed by its binding to its receptor ALK3 through Native PAGE and ELISA assay using BMP2 specific antibody. It is possible to obtain BMP2 expression in soluble active form by using molecular and chemical chaperons which work synergistically in bacterial cells to fold disulphide-rich proteins at low temperature in easy and time saving steps (18 ̊C).

In-silico drug repurposing for targeting SARS-CoV-2 main protease (Mpro)

COVID-19, caused by novel coronavirus or SARS-CoV-2, is a viral disease which has infected millions worldwide. Considering the urgent need of the drug for fighting against this infectious disease, we have performed in-silico drug repurposing followed by molecular dynamics (MD) simulation and MM-GBSA calculation. The main protease (Mpro) is one of the best-characterized drug targets among coronaviruses, therefore, this was screened for already known FDA approved drugs and some natural compounds. Comparison of docking and MD simulation results of complexes of drugs with that of inhibitor N3 (experimentally obtained) suggests EGCG, withaferin, dolutegravir, artesunate as potential inhibitors of the main protease (Mpro). Further, in silico docking and MD simulation suggest that EGCG analogues ZINC21992196 and ZINC 169337541 may act as a better inhibitor.Communicated by Ramaswamy H. Sarma.

Kinetics theories to understand the mechanism of aggregation of a protein and to design strategies for its inhibition

Protein aggregation phenomenon is closely related to the formation of amyloids which results in many neurodegenerative diseases like Alzheimer's, Parkinson's, Huntington's, and Amyotrophic Lateral Sclerosis. In order to prevent and treat these diseases, a clear understanding of the mechanism of misfolding and self-assembly of peptides and proteins is very crucial. The aggregation of a protein may involve various microscopic events. Multiple simulations utilizing the solutions of the master equation have given a better understanding of the kinetic profiles involved in the presence and absence of a particular microscopic event. This review focuses on understanding the contribution of these molecular events to protein aggregation based on the analysis of kinetic profiles of aggregation. We also discuss the effect of inhibitors, which target various species of aggregation pathways, on the kinetic profile of protein aggregation. At the end of this review, some strategies for the inhibition of aggregation that can be utilized by combining the chemical kinetics approach with thermodynamics are proposed.

An improved strategy of TGFβ3 expression in Escherichia coli: Exploiting folding modulators for a switch from misfolded to folded form

Transforming growth factor beta 3 (TGFβ3) exhibits a complex native structure featuring the presence of multiple disulfide bonds forming the active dimer. Consequently, its heterologous expression in microbial system invariably leads to inclusion body (IB) formation. In this study, we observed an interesting phenomenon of switching a significant fraction of misfolded TGFβ3 to folded form by modulating the cellular protein folding machinery. We carried out co-expression experiments with chaperones and demonstrated the requirement of a coordinated action of DnaK-DnaJ-GrpE and GroESL, to achieve the native soluble conformation of TGFβ3, during over-expression in E. coli. The novelty of this study lies in the fact that orchestration of a group of chaperones to work in concert for efficient folding and assembly of TGFβ3-like cytokines has not been widely explored. Additionally, we have also demonstrated that presence of osmolytes (sorbitol or trehalose) in the growth media have an appreciable impact on the solubility of TGFβ3. We have further shown a synergism between the effects of molecular chaperone and osmolytes on the solubility of TGFβ3. We have confirmed the functionality of soluble TGFβ3 by performing binding interactions with its cognate receptor TβRII. Our study delineates the fact that an effective combination of chaperones or optimum concentration of compatible osmolyte, can efficiently abrogate competing aggregation pathways and help attain the native conformation of a cysteine rich cytokine in a facile manner.

Stimulation of GMP formation in hGBP1 is mediated by W79 and its effect on the antiviral activity

Interferon-inducible large GTPases are critical for innate immunity. The distinctive feature of a large GTPase, human guanylate binding protein-1 (hGBP1), is the sequential hydrolysis of GTP into GMP via GDP. Despite several structural and biochemical studies, the underlying mechanism of assembly-stimulated GMP formation by hGBP1 and its role in immunity are not fully clarified. Using a series of biochemical, biophysical, and in silico experiments, we studied four tryptophan residues, located near switch I-II (in and around the active site) to understand the conformational changes near these regions and also to investigate their effect on enhanced GMP formation. The W79A mutation showed significantly reduced GMP formation, whereas the W81A and W180A substitutions exhibited only a marginal defect. The W114A mutation showed a long-range effect of further enhanced GMP formation, which was mediated through W79. We also observed that after first phosphate cleavage, the W79-containing region undergoes a conformational change, which is essential for stimulated GMP formation. We suggest that this conformational change helps to reposition the active site for the next cleavage step, which occurs through a stable contact between the indole moiety of W79 and the main chain carbonyl of K76. We also showed that stimulated GMP formation is crucial for antiviral activity against hepatitis C. Thus, the present study not only provides new insight for the stimulation of GMP formation in hGBP1, but also highlights the importance of the enhanced second phosphate cleavage product in the antiviral activity.

Interaction of TGFβ3 ligand with its receptors type II (TβRII) and type I (TβRI): A unique mechanism of protein-protein association

The proper orchestration of transforming growth factor beta (TGFβ) mediated signal transduction depends upon a delicate set of interactions between specific ligands and their receptors. Here we present an in-depth profiling of the binding mechanism of TGFβ3 ligand with its type II and type I receptors (TβRII and TβRI) using isothermal titration calorimetry (ITC). Studies were carried out in acidic pH as it has great physiological relevance for TGFβ3 activity. Our findings reveal an unusual positive enthalpy (∆H) compensated by a large favourable entropy (∆S) during TGFβ3-TβRII interaction. In addition to the hydrophobic effect, we propose that a distinct conformational switch from "closed" to "open" form as experienced by TGFβ3 on binding to TβRII is contributing significantly to the increase in overall entropy of the system. Binding studies of TGFβ3 and TβRII were carried out at different pH values and salt concentrations to gain further insight into the thermodynamics of the interaction. Furthermore, the importance of hydrophobic interactions on the binding affinity of TβRII with TGFβ3 was confirmed by two TβRII variants (interfacial). Finally, a distinct shift from entropy to enthalpy dominated interaction was observed upon recruitment of TβRI to the binary complex forming the ternary complex.

Quercetin and Baicalein Act as Potent Antiamyloidogenic and Fibril Destabilizing Agents for SOD1 Fibrils

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease that has been associated with the deposition of aggregates of superoxide dismutase 1 (SOD1). Effective therapeutics against SOD1 fibrillation is still an area of active research. Herein, we demonstrate the potential of two naturally occurring flavonoids (quercetin and baicalein) to inhibit fibrillation of wild-type SOD1 with the aid of a series of biophysical techniques. Our seeding experiments reveal that both of these flavonoids significantly affect the fibril elongation. Interestingly, our ThT binding assay, TEM, and SDS-PAGE experiments suggest that these flavonoids also disintegrate the fibrils into shorter fragments but do not completely depolymerize them into monomers. Binding parameters obtained from the analysis of UV-vis spectra suggest that these flavonoids bind moderately to native SOD1 dimer and have different binding sites. Docking of these flavonoids with a non-native monomer, non-native trimer, and oligomer derived from the 11-residue segment of SOD1 indicates that both quercetin and baicalein can bind to these species and thus can arrest the elongation of fibrils by blocking the fibrillar core regions on the intermediate species formed during aggregation of SOD1. MTT assay data revealed that both the flavonoids reduced the cytotoxicity of SOD1 fibrils. Experimental data also show the antiamyloidogenic potential of both flavonoids against A4V SOD1 mutant fibrillation. Thus, our findings may provide a direction for designing effective therapeutic agents against ALS which can act as promising antiamyloidogenic and fibril destabilizing agents.

Thinking beyond tradition: Polyphenols as effective refolding modulators

Despite polyphenols having had proven roles as amyloid alleviators their service has rarely been made use of in protein refolding/renaturation thus far, where aggregation can be a major competing pathway. TGFβ3, expressed in inclusion bodies, is a classical example of a protein prone to high rate of aggregation severely limiting its refolding yield owing to its large cysteine content and structural complexity. Here, we have used various polyphenols (EGCG, baicalein, myricetin) either alone or in combination with the pseudo-chaperone beta cyclodextrin, in the refolding buffer. With the help of non-reducing SDS PAGE and size exclusion chromatography, we showed that refolding in the presence of baicalein or EGCG along with βCD indeed increase the yield of the native protein in a time dependent manner. EGCG expedites the refolding process giving a maximum increase of the refolding yield within 24 h while baicalein takes as long as 48 h for the same. The mechanism of mode of actions of polyphenols during refolding was further delineated by ITC. The effect of polyphenols on the aggregation kinetics and stability of native TGFβ3 were also explored. Thus these small molecules provide a promising alternate route in increasing the yield of aggregation prone proteins during refolding.

Adsorption of unfolded Cu/Zn superoxide dismutase onto hydrophobic surfaces catalyzes its formation of amyloid fibrils

Intracellular aggregates of superoxide dismutase 1 (SOD1) are associated with amyotrophic lateral sclerosis. In vivo, aggregation occurs in a complex and dense molecular environment with chemically heterogeneous surfaces. To investigate how SOD1 fibril formation is affected by surfaces, we used an in vitro model system enabling us to vary the molecular features of both SOD1 and the surfaces, as well as the surface area. We compared fibril formation in hydrophilic and hydrophobic sample wells, as a function of denaturant concentration and extraneous hydrophobic surface area. In the presence of hydrophobic surfaces, SOD1 unfolding promotes fibril nucleation. By contrast, in the presence of hydrophilic surfaces, increasing denaturant concentration retards the onset of fibril formation. We conclude that the mechanism of fibril formation depends on the surrounding surfaces and that the nucleating species might correspond to different conformational states of SOD1 depending on the nature of these surfaces.

A computational approach to get insights into multiple faces of additives in modulation of protein aggregation pathways

An enormous population worldwide is presently confronted with debilitating neurodegenerative diseases. The etiology of the disease is connected to protein aggregation and the events involved therein. Thus, a complete understanding of an inhibitor at different stages in the process is imperative for the formulation of a drug molecule. This review presents a detailed summary of the current status of different cosolvents. It further develops how the complex aggregation pathway can be simplified into three steps common to all proteins and the way computer simulations can be exploited to gain insights into the ways by which known inhibitors can affect all these stages. Computation of theoretical parameters in this regard and their correlation with experimental techniques is accentuated. In addition to providing an outline of the scope of different additives, this review showcases the way by which the problem of analyzing an effect of an additive can be addressed effectively via MD simulations.

Stimulation of heat shock protein 90 chaperone function through binding of a novobiocin analog KU-32

Heat shock protein 90 (Hsp90) is a eukaryotic chaperone responsible for the folding and functional activation of numerous client proteins, many of which are oncoproteins. Thus, Hsp90 inhibition has been intensely pursued, resulting in the development of many potential Hsp90 inhibitors, not all of which are well-characterized. Hsp90 inhibitors not only abrogate its chaperone functions, but also could help us gain insight into the structure-function relationship of this chaperone. Here, using biochemical and cell-based assays along with isothermal titration calorimetry, we investigate KU-32, a derivative of the Hsp90 inhibitor novobiocin (NB), for its ability to modulate Hsp90 chaperone function. Although NB and KU-32 differ only slightly in structure, we found that upon binding, they induce completely opposite conformational changes in Hsp90. We observed that NB and KU-32 both bind to the C-terminal domain of Hsp90, but surprisingly, KU-32 stimulated the chaperone functions of Hsp90 via allosteric modulation of its N-terminal domain, responsible for the chaperone's ATPase activity. In vitro and in silico studies indicated that upon KU-32 binding, Hsp90 undergoes global structural changes leading to the formation of a "partially closed" intermediate that selectively binds ATP and increases ATPase activity. We also report that KU-32 promotes HeLa cell survival and enhances the refolding of an Hsp90 substrate inside the cell. This discovery explains the effectiveness of KU-32 analogs in the management of neuropathies and may facilitate the design of molecules that promote cell survival by enhancing Hsp90 chaperone function and reducing the load of misfolded proteins in cells.

Tuning the Balance between Fibrillation and Oligomerization of α-Synuclein in the Presence of Dopamine

The aggregates of α-synuclein bear a close connection with Parkinson's disease, which is largely characterized by the loss of the dopaminergic neurons. Dopamine promotes the formation of undesirable sodium dodecyl sulfate (SDS)-resistant oligomers of α-synuclein. In this study, we have shown that the inhibition of fibrillation by an additive may not always be the ultimate deciding factor in the context of its potential as a successful additive. Copper promotes the fibrillation of α-synuclein in buffer alone but inhibits the formation of SDS-resistant oligomers in the presence of dopamine. Glycerol, on the other hand, increases the population of such dopamine-mediated SDS-resistant oligomers. We speculate such an effect to be a manifestation of the distinct oxidation pathway of dopamine in the presence of copper.

Paradoxical Effect of Trehalose on the Aggregation of α-Synuclein: Expedites Onset of Aggregation yet Reduces Fibril Load

Aggregation of α-synuclein is closely connected to the pathology of Parkinson's disease. The phenomenon involves multiple steps, commenced by partial misfolding and eventually leading to mature amyloid fibril formation. Trehalose, a widely accepted osmolyte, has been shown previously to inhibit aggregation of various globular proteins owing to its ability to prevent the initial unfolding of protein. In this study, we have examined if it behaves in a similar fashion with intrinsically disordered protein α-synuclein and possesses the potential to act as therapeutic agent against Parkinson's disease. It was observed experimentally that samples coincubated with trehalose fibrillate faster compared to the case in its absence. Molecular dynamics simulations suggested that this initial acceleration is manifestation of trehalose's tendency to perturb the conformational transitions between different conformers of monomeric protein. It stabilizes the aggregation prone "extended" conformer of α-synuclein, by binding to its exposed acidic residues of the C terminus. It also favors the β-rich oligomers once formed. Interestingly, the total fibrils formed are still promisingly less since it accelerates the competing pathway toward formation of amorphous aggregates.

Role of Tryptophan in Protein–Nanocrystals Interaction: Energy or Charge Transfer

The understanding of the interaction between the semiconductor nanocrystals (NCs) and the proteins are essential for design and fabrication of nanocomposites for application in the field of biotechnology. Herein, we have studied the interaction between CdTe NCs and the proteins by steady-state and time-resolved photoluminescence (PL) spectroscopy. The steady-state PL intensity of CdTe NCs is quenched and enhanced in the presence of lysozyme and bovine serum albumin, respectively. However, the PL intensity of CdTe NCs is not affected with α-synuclein, indicating the role of tryptophan moiety in the protein–NCs interaction. The detailed analysis of PL data allows us to elucidate the dominant mechanism of interaction, i.e. charge or energy transfer, depending on the location of tryptophan residues in the protein. Assuming a Poisson statistic of lysozymes around NCs, the Poisson binding model is used to understand the kinetics of charge transfer from CdTe NCs to the lysozyme. It provides the average number of lysozymes present on the surface of one CdTe NC.

Inhibition of GNNQQNY prion peptide aggregation by trehalose: a mechanistic view

Deposition of amyloid fibrils is the seminal event in the pathogenesis of numerous neurodegenerative diseases. The formation of this amyloid assembly is the manifestation of a cascade of structural transitions including toxic oligomer formation in the early stages of aggregation. Thus a viable therapeutic strategy involves the use of small molecular ligands to interfere with this assembly. In this perspective, we have explored the kinetics of aggregate formation of the fibril forming GNNQQNY peptide fragment from the yeast prion protein SUP35 using multiple all atom MD simulations with explicit solvent and provided mechanistic insights into the way trehalose, an experimentally known aggregation inhibitor, modulates the aggregation pathway. The results suggest that the assimilation process is impeded by different barriers at smaller and larger oligomeric sizes: the initial one being easily surpassed at higher temperatures and peptide concentrations. The kinetic profile demonstrates that trehalose delays the aggregation process by increasing both these activation barriers, specifically the latter one. It increases the sampling of small-sized aggregates that lack the beta sheet conformation. Analysis reveals that the barrier in the growth of larger stable oligomers causes the formation of multiple stable small oligomers which then fuse together bimolecularly. The PCA of 26 properties was carried out to deconvolute the events within the temporary lag phases, which suggested dynamism in lags involving an increase in interchain contacts and burial of SASA. The predominant growth route is monomer addition, which changes to condensation on account of a large number of depolymerisation events in the presence of trehalose. The favourable interaction of trehalose specifically with the sidechain of the peptide promotes crowding of trehalose molecules in its vicinity - the combination of both these factors imparts the observed behaviour. Furthermore, increasing trehalose concentration leads to faster expulsion of water molecules than interpeptide interactions. These expelled water molecules have larger translational movement, suggesting an entropy factor to favor the assembly process. Different conformations observed under this condition suggest the role of water molecules in guiding the morphology of the aggregates as well. A similar scenario exists on increasing peptide concentration.

Cu/Zn Superoxide Dismutase Forms Amyloid Fibrils under Near-Physiological Quiescent Conditions: The Roles of Disulfide Bonds and Effects of Denaturant

Cu/Zn superoxide dismutase (SOD1) forms intracellular aggregates that are pathological indicators of amyotrophic lateral sclerosis. A large body of research indicates that the entry point to aggregate formation is a monomeric, metal-ion free (apo), and disulfide-reduced species. Fibril formation by SOD1 in vitro has typically been reported only for harsh solvent conditions or mechanical agitation. Here we show that monomeric apo-SOD1 in the disulfide-reduced state forms fibrillar aggregates under near-physiological quiescent conditions. Monomeric apo-SOD1 with an intact intramolecular disulfide bond is highly resistant to aggregation under the same conditions. A cysteine-free variant of SOD1 exhibits fibrillization behavior and fibril morphology identical to those of disulfide-reduced SOD1, firmly establishing that intermolecular disulfide bonds or intramolecular disulfide shuffling are not required for aggregation and fibril formation. The decreased lag time for fibril formation resulting from reduction of the intramolecular disulfide bond thus primarily reflects the decreased stability of the folded state relative to partially unfolded states, rather than an active role of free sulfhydryl groups in mediating aggregation. Addition of urea to increase the amount of fully unfolded SOD1 increases the lag time for fibril formation, indicating that the population of this species does not dominate over other factors in determining the onset of aggregation. Our results contrast with previous results obtained for agitated samples, in which case amyloid formation was accelerated by denaturant. We reconcile these observations by suggesting that denaturants destabilize monomeric and aggregated species to different extents and thus affect nucleation and growth.

Plant derived antimicrobial peptide Ib-AMP1 as a potential alternative drug candidate for Staphylococcus aureus toxins

Due to an increase in the occurrence of multi drug resistant microorganisms a need for the development of alternative drugs comes in light. This alternative drug should be such that the microorganisms should not be able to develop resistance against them easily. Antimicrobial peptides are the most potential candidates to be developed as alternative drug. In the present study the three toxins ETA, ETB and PVL of Staphylococcus aureus were docked with four antimicrobial peptides, Ib-AMP1, JCPep7, Snakin2, Sesquin, derived from plants. The docking studies predict that Ib-AMP1 shows significant interactions with all these three toxins. Hence, further studies can be carried out for developing Ib-AMP1 as an alternative drug against the toxins of Staphylococcus aureus.

Efficacy and Stability studies of microbial folate fortified fruit juices prepared using probiotic microorganism

Folate, natural form of water soluble vitamin folic acid, is significant for humans as involved in most important metabolic reactions i.e. nucleotide synthesis and amino acid inter conversions. Thus its deficiency causes neural tube defects in newborns and cardiovascular diseases, and cancers. Humans cannot synthesize folate de novo so consumption through diet is essential. Natural food sources, supplements and fortified food products are the choices available to complete the Daily recommended intake. However microbial fortification using probiotics recently gained wide attention due to dual advantage of natural food matrix with enhanced folate content along with the probiotics benefits. Current study was focused on the microbial fortification of fruit juices and their efficacy and stability studies. Freshly filtered orange and tomato juice was prepared and inoculated with Streptococcus thermophilus NCIM 2904. Incubation was done at 40°C and samples were collected at different time interval. Folate extraction was done using human plasma and content was measured by microbiological assay using Lactobacillus casei NCIM No. 2364. Efficacy and stability studies were carried out to ensure the quality of juices to be consumed in terms of folate content, viable cell count and pH after 4 weeks of storage at low temperature. Positive results were observed as folate content was quite stable whereas viable cell count was also found to be significant till some time without adding any preservatives. The results indicated that fortified fruit juices could be used as probiotic beverages with enhanced folate content.

CD11b activation suppresses TLR-dependent inflammation and autoimmunity in systemic lupus erythematosus

Genetic variations in the ITGAM gene (encoding CD11b) strongly associate with risk for systemic lupus erythematosus (SLE). Here we have shown that 3 nonsynonymous ITGAM variants that produce defective CD11b associate with elevated levels of type I interferon (IFN-I) in lupus, suggesting a direct link between reduced CD11b activity and the chronically increased inflammatory status in patients. Treatment with the small-molecule CD11b agonist LA1 led to partial integrin activation, reduced IFN-I responses in WT but not CD11b-deficient mice, and protected lupus-prone MRL/Lpr mice from end-organ injury. CD11b activation reduced TLR-dependent proinflammatory signaling in leukocytes and suppressed IFN-I signaling via an AKT/FOXO3/IFN regulatory factor 3/7 pathway. TLR-stimulated macrophages from CD11B SNP carriers showed increased basal expression of IFN regulatory factor 7 (IRF7) and IFN-β, as well as increased nuclear exclusion of FOXO3, which was suppressed by LA1-dependent activation of CD11b. This suggests that pharmacologic activation of CD11b could be a potential mechanism for developing SLE therapeutics.

In vitro evaluation of shear bond strength and microleakage of different pit and fissure sealants

Aim and Objectives:

Fissure caries is most common in children due to deep pit and fissures. Pit and fissure areas on the occlusal surface of the teeth make them susceptible to dental caries, which need to be prevented or restored. Fissures sealant reduces the risk of occlusal caries. The present study was done to evaluate microleakage and shear bond strength of various fissure sealants.

Materials and Methods:

Thirty-six extracted molars were randomly allocated equally (n = 12) into three groups with three different sealants to evaluate shear bond strength and microleakage at sealant space. The shear bond strengths was evaluated with one-way analysis of variance and microleakage by Kruskal-Wallis nonparametric test using the Statistical Package for the Social Sciences version 18.0 (Chicago: SPSS Inc, 2009).

Results:

Tetric flow (16.8 MPa) recorded the highest shear bond strength and the difference was statistically significant with enamel loc (12.8 MPa). There was no statistically significant difference in relation to microleakage (P > 0.05) in the tested groups.

Conclusions:

Tetric flow recorded the highest shear bond strength and the difference was statistically significant with enamel loc. However, there was no statistically significant difference among the groups regarding microleakage.

Glycerol inhibits the primary pathways and transforms the secondary pathway of insulin aggregation

Aggregation of insulin initiated from the monomeric form proceeds via the secondary pathway of fragmentation. It was interesting to find that glycerol had the potential to transform the secondary pathway of aggregation from fragmentation to heterogeneous nucleation in a concentration dependent manner. Such a change in the secondary pathway was manifested by a change in the fibrillar morphology, wherein, longer fibrils were formed in the presence of glycerol. Glycerol could inhibit all the major steps of insulin aggregation. The analysis of the kinetic traces suggested that the inhibitory effect was most significant on the primary pathways, although secondary nucleation and elongation were also inhibited. In fact, at higher glycerol concentrations, the primary pathways were inhibited to such an extent that the majority of the aggregation was now driven by the secondary pathways. Our data suggest that glycerol binds to the early intermediates in the insulin aggregation pathway, and inhibits them from forming the aggregation competent species capable of elongation. As higher order species are formed in the aggregation pathway, the relative stabilization rendered by glycerol diminishes due to the exclusion of glycerol from the interface.

Effect of pH and temperature on conformational equilibria and aggregation behaviour of curcumin in aqueous binary mixtures of ethanol

Conformational equilibria of curcumin, a potential therapeutic agent, can be modulated by changing pH, temperature and solvent composition.

Differential influence of additives on the various stages of insulin aggregation

The different species in the aggregation pathway of insulin are stabilized/destabilized to different extent in the presence of various additives.

Modulations in the self-assembly of bovine serum albumin by enhanced depolymerisation and condensation induced upon stirring

An unusual phenomenon in the aggregation profile of BSA in the presence of CTAB, brought about by stirring, is reported here.

Revisiting the conundrum of trehalose stabilization

Protein aggregation and loss of protein's biological functionality are manifestations of protein instability. Cosolvents, in particular trehalose, are widely accepted antidotes against such destabilization. Although numerous theories have been promulgated in the literature with regard to its mechanism of stabilization, the present scenario is still elusive in view of the discrepancies existing in them. To this end, we have revisited the conundrum and attempted to rationalize the mechanism by conducting thorough investigation of the effect of trehalose on the native, partially unfolded and denatured states of protein "Lysozyme" by means of molecular dynamic (MD) simulations under different temperature and concentration regimes. Two-dimensional contour plots along with principal component analysis suggest that trehalose molecules offer on-pathway stabilization unaltering the principal direction of protein's motion, although it slows down protein dynamics so that the protein gets trapped in the homogeneous ensemble of conformations closer to the native state. Free energy landscape reveals higher population of native compared to intermediate and denatured states. Delphi results and calculation of the preferential interaction parameter demonstrate that this relative stabilization of the native state can be ascribed to be the consequence of favourable interactions of trehalose with side chains of certain loci on the protein surface encompassing polar flexible residues. Stability of protein results from the observed difference in binding affinity of trehalose for native and denatured states of protein. Our findings are at variance with the common conception of relative destabilization of the denatured state. Rather, we provide evidence for relative stabilization of the native state. This stabilization is due to interplay of protein-trehalose, water-trehalose, water-water, protein-water and trehalose-trehalose interactions.

Curcumin binds to the pre-fibrillar aggregates of Cu/Zn superoxide dismutase (SOD1) and alters its amyloidogenic pathway resulting in reduced cytotoxicity

Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease that affects motor neurons. Unfortunately, effective therapeutics against this disease is still not available. Almost 20% of familial ALS (fALS) is suggested to be associated with pathological deposition of superoxide dismutase (SOD1). Evidences suggest that SOD1-containing pathological inclusions in ALS exhibit amyloid like properties. An effective strategy to combat ALS may be to inhibit amyloid formation of SOD1 using small molecules. In the present study, we observed the fibrillation of one of the premature forms of SOD1 (SOD1 with reduced disulfide) in the presence of curcumin. Using ThT binding assay, AFM, TEM images and FTIR, we demonstrate that curcumin inhibits the DTT-induced fibrillation of SOD1 and favors the formation of smaller and disordered aggregates of SOD1. The enhancement in curcumin fluorescence on the addition of oligomers and pre-fibrillar aggregates of SOD1 suggests binding of these species to curcumin. Docking studies indicate that putative binding site of curcumin may be the amyloidogenic regions of SOD1. Further, there is a significant increase in SOD1 mediated toxicity in the regime of pre-fibrillar and fibrillar aggregates which is not evident in curcumin containing samples. All these data suggest that curcumin reduces toxicity by binding to the amyloidogenic regions of the species on the aggregation pathway and blocking the formation of the toxic species. Nanoparticles of curcumin with higher aqueous solubility show similar aggregation control as that of curcumin bulk. This suggests a potential role for curcumin in the treatment of ALS.

Salt mediated unusual switching in the aggregation kinetic profile of human carbonic anhydrase

Aggregation pathway of human carbonic anhydrase II in the presence of salt.

Transforming growth factor receptor type II (ec-TβR II) behaves as a halophile

The members of transforming growth factor β family (TGF-β) are multifunctional proteins but their main role is to control cell proliferation and differentiation. Polypeptides of TGF-β family function by binding to two related, functionally distinct transmembrane receptor kinases, first to the type II (TβR II) followed by type I receptor (TβR I). The paper describes, in details, the stability of wt-ec-TβR II under different conditions. The stability of wt-ec-TβR II was observed at different pH and salt concentration using fluorescence spectroscopy. Stability of ec-TβR II decreases with decrease in pH. Interestingly, the addition of salt increases the stability of the TβRII at pH 5.0 as observed for halophiles. Computational analysis using DELPHI suggests that this is probably due to the decrease in repulsion between negatively charged residues at surface on the addition of salt. This is further confirmed by the change in the stability of receptor on mutation of some of the residues (D32A) at surface.

Agonist leukadherin-1 increases CD11b/CD18-dependent adhesion via membrane tethers

Integrin CD11b/CD18 is a key adhesion receptor that mediates leukocyte migration and immune functions. Leukadherin-1 (LA1) is a small molecule agonist that enhances CD11b/CD18-dependent cell adhesion to its ligand ICAM-1. Here, we used single-molecule force spectroscopy to investigate the biophysical mechanism by which LA1-activated CD11b/CD18 mediates leukocyte adhesion. Between the two distinct populations of CD11b/CD18:ICAM-1 complex that participate in cell adhesion, the cytoskeleton(CSK)-anchored elastic elements and the membrane tethers, we found that LA1 enhanced binding of CD11b/CD18 on K562 cells to ICAM-1 via the formation of long membrane tethers, whereas Mn(2+) additionally increased ICAM-1 binding via CSK-anchored bonds. LA1 activated wild-type and LFA1(-/-) neutrophils also showed longer detachment distances and time from ICAM-1-coated atomic force microscopy tips, but significantly lower detachment force, as compared to the Mn(2+)-activated cells, confirming that LA1 primarily increased membrane-tether bonds to enhance CD11b/CD18:ICAM-1 binding, whereas Mn(2+) induced additional CSK-anchored bond formation. The results suggest that the two types of agonists differentially activate integrins and couple them to the cellular machinery, providing what we feel are new insights into signal mechanotransduction by such agents.

Insight into temperature dependence of GTPase activity in human guanylate binding protein-1

Interferon-γ induced human guanylate binding protein-1(hGBP1) belongs to a family of dynamin related large GTPases. Unlike all other GTPases, hGBP1 hydrolyzes GTP to a mixture of GDP and GMP with GMP being the major product at 37°C but GDP became significant when the hydrolysis reaction was carried out at 15°C. The hydrolysis reaction in hGBP1 is believed to involve with a number of catalytic steps. To investigate the effect of temperature in the product formation and on the different catalytic complexes of hGBP1, we carried out temperature dependent GTPase assays, mutational analysis, chemical and thermal denaturation studies. The Arrhenius plot for both GDP and GMP interestingly showed nonlinear behaviour, suggesting that the product formation from the GTP-bound enzyme complex is associated with at least more than one step. The negative activation energy for GDP formation and GTPase assay with external GDP together indicate that GDP formation occurs through the reversible dissociation of GDP-bound enzyme dimer to monomer, which further reversibly dissociates to give the product. Denaturation studies of different catalytic complexes show that unlike other complexes the free energy of GDP-bound hGBP1 decreases significantly at lower temperature. GDP formation is found to be dependent on the free energy of the GDP-bound enzyme complex. The decrease in the free energy of this complex at low temperature compared to at high is the reason for higher GDP formation at low temperature. Thermal denaturation studies also suggest that the difference in the free energy of the GTP-bound enzyme dimer compared to its monomer plays a crucial role in the product formation; higher stability favours GMP but lower favours GDP. Thus, this study provides the first thermodynamic insight into the effect of temperature in the product formation of hGBP1.