Dimerization of Full-length Aß -42 Peptide: A Comparison of Different Force Fields and Water Models.

Among the two isoforms of amyloid- i.e., Aß-40 and Aß-42, Aß-42 is more toxic due to its increased aggregation propensity. The oligomerization pathways of amyloid-ß may be investigated by studying its dimerization process at an atomic level. Intrinsically disordered proteins (IDPs) lack well-defined structures and are associated with numerous neurodegenerative disorders. Molecular dynamics simulations of these proteins are often limited by the choice of parameters due to inconsistencies in the empirically developed protein force fields and water models. To evaluate the accuracy of recently developed force fields for IDPs, we study the dimerization of full-length Aß-42 in aqueous solution with three different combinations of AMBER force field parameters and water models such as ff14SB/TIP3P, ff19SB/OPC, and ff19SB/TIP3P using classical MD and Umbrella Sampling method. This work may be used as a benchmark to compare the performance of different force fields for the simulations of IDPs.

Muco-Adhesive and Muco-Penetrative Formulations for the Oral Delivery of Insulin.

Insulin, a pivotal anabolic hormone, regulates glucose homeostasis by facilitating the conversion of blood glucose to energy or storage. Dysfunction in insulin activity, often associated with pancreatic ß cells impairment, leads to hyperglycemia, a hallmark of diabetes. Type 1 diabetes (T1D) results from autoimmune destruction of ß cells, while type 2 diabetes (T2D) stems from genetic, environmental, and lifestyle factors causing ß cell dysfunction and insulin resistance. Currently, insulin therapy is used for most of the cases of T1D, while it is used only in a few persistent cases of T2D, often supplemented with dietary and lifestyle changes. The key challenge in oral insulin delivery lies in overcoming gastrointestinal (GI) barriers, including enzymatic degradation, low permeability, food interactions, low bioavailability, and long-term safety concerns. The muco-adhesive (MA) and muco-penetrative (MP) formulations aim to enhance oral insulin delivery by addressing these challenges. The mucus layer, a hydrogel matrix covering epithelial cells in the GI tract, poses significant barriers to oral insulin absorption. Its structure, composition, and turnover rate influence interactions with insulin and other drug carriers. Some of the few factors that influence mucoadhesion and mucopenetration are particle size, surface charge distribution, and surface modifications. This review discusses the challenges associated with oral insulin delivery, explores the properties of mucus, and evaluates the strategies for achieving excellent MA and MP formulations, focusing on nanotechnology-based approaches. The development of effective oral insulin formulations holds the potential to revolutionize diabetes management, providing patients with a more convenient and patient-friendly alternative to traditional insulin administration methods.

Molecular Dynamics Simulation Study of the Self-Assembly of Tau-Derived PHF6 and Its Inhibition by Oleuropein Aglycone from Extra Virgin Olive Oil.

Alzheimer's disease (AD) and other taupathies are neurodegenerative disorders associated with the amyloid deposition of the Tau protein in the brain. This amyloid formation may be inhibited by small molecules, which is recognized as one of the best therapeutic strategies to stop the progression of the disease. This work focuses on the small nucleating segment, hexapeptide-paired helical filament 6 (PHF6), responsible for Tau aggregation. Using computational modeling and classical molecular dynamics simulations, we show that PHF6 monomers collapse in water to form ß-sheet rich structures, and the main olive oil polyphenol oleuropein aglycone (OleA) prevents peptide aggregation significantly. We gradually increase the ratio of the PHF6-OleA from 1:1 to 1:3 and find that for the 1:1 ratio, the peptide monomers are prone to form aggregated structures, while for the 1:2 ratio, the formation of the extended ß-sheet structure is significantly less. For a 1:3 ratio of protein/OleA, the peptide residues are sufficiently crowded by OleA molecules through hydrogen bonding, hydrophobic interactions, and π-π stacking; hence, the peptide chains prefer to exist in a monomeric random coil conformation.

Impact of Oxysterols in Age-Related Disorders and Strategies to Alleviate Adverse Effects.

Oxysterols or cholesterol oxidation products are a class of molecules with the sterol moiety, derived from oxidative reaction of cholesterol through enzymatic and non-enzymatic processes. They are widely reported in animal-origin foods and prove significant involvement in the regulation of cholesterol homeostasis, lipid transport, cellular signaling, and other physiological processes. Reports of oxysterol-mediated cytotoxicity are in abundance and thus consequently implicated in several age-related and lifestyle disorders such as cardiovascular diseases, bone disorders, pancreatic disorders, age-related macular degeneration, cataract, neurodegenerative disorders such as Alzheimer's and Parkinson's disease, and some types of cancers. In this chapter, we attempt to review a selection of physiologically relevant oxysterols, with a focus on their formation, properties, and roles in health and disease, while also delving into the potential of natural and synthetic molecules along with bacterial enzymes for mitigating oxysterol-mediated cell damage.

Curvature induced structural changes of the chicken villin headpiece subdomain by single walled carbon nanotubes.

Carbon nanotubes (CNTs) are identified as potential candidates for drug and biomolecular loading and delivery. CNTs of different chiralities have different diameters, which may significantly affect their abilities to interact with different types of biomolecules. Herein, we employ classical molecular dynamics simulation to provide insight into the curvature-dependent interactions between a model protein, chicken villin headpiece subdomain (HP36), with CNTs having chiralities (8,8), (12,12), and (20,20). It is revealed that, with increasing radii, the protein encounters more aromatic carbon atoms on the surface of the CNT, leading to its increasing strength of adsorption. However, the extent of adsorption has a limiting magnitude, after which an increase in the radius of the nanotube has practically no effect on the extent of adsorption. Spontaneous encapsulation of the protein was demonstrated using a (28,28) CNT, where the protein is found to undergo insignificant structural perturbation. Finally, steered molecular dynamics simulations have been performed to mimic the force-induced release of the protein from within the nanotube cavity. It has been identified that a minimum force of ∼300 pN and a minimum velocity of 4 Šns-1 are required to release the protein from the CNT at 300 K. Any external force below the critical magnitude and inducing velocity less than 4 Šns-1 allows the translocation of the protein through the inner surface of the CNT; however, before being released, the protein undergoes unfolding, thereby losing the secondary structure and biological activity.

Molecular insights into the urea-choline-O-sulfate interactions in aqueous solution.

Urea and choline-O-sulfate (COS) are both osmolytes, but have opposite effects on protein structure. Urea has been well-known for years to destabilize protein structure. Though COS has been revealed as an osmoprotective molecule against urea induced denaturation of proteins, the mechanism of this compensation is still unexplored. This study focuses on a theoretical investigation of the interdependent behavior of urea and COS in a mixture, to explore how urea becomes a weaker denaturing agent in the presence of COS. In this study, we have considered every possible interaction among the solute (urea and COS) and solvent (water) both at room temperature and high temperature, employing two different force field parameters i.e., CHARMM General Force Field parameters (CGenFF) and General AMBER Force Field (GAFF) parameters through classical molecular dynamics simulation studies. Different techniques have been used to analyze the average interactions between COS and urea as well as their solvation properties, which show that in the presence of COS, urea becomes a less effective denaturant than when alone. The water-water interaction shows that the mixed osmolyte solution of urea and COS strengthens the water hydrogen bonding network. The enhanced solvation of urea and COS in the urea-COS mixture and their mutual interactions, results in the exclusion of free urea as well as COS from the solution. This synergistic behavior of urea and COS could be the major reason behind COS counteracting urea's denaturation of proteins.

Controlling the self-assembly of human calcitonin: a theoretical approach using molecular dynamics simulations.

Human calcitonin (hCT) is a 32-residue amino acid poly-peptide hormone which is secreted by the C-cells (also known as parafollicular cells) of thyroid glands. It acts to inhibit osteoclast cell hormones by reducing the cell function and regulating calcium and phosphate in blood. hCT has a high tendency to assemble into protofilaments with ß-sheet conformations. Amyloid fibril formation of hCT reduces its bio-activity and limits its application as a therapeutic drug. Salmon calcitonin (sCT), which also carries the same disulfide bridge at the N and C-terminus, but differs at the 16 residue position from hCT, has less propensity to aggregate than hCT. Human calcitonin has much higher bio-activity than sCT if its aggregation propensity is reduced. Substituting the key residues which are responsible for the aggregation of hCT, is one of the ways to reduce its aggregation and fibril formation. hCT analogues with less aggregation tendency can be exploited as therapeutic drugs. In this work, we study the amyloidogenic behavior of hCT and its peptide based derivatives i.e., sCT, phCT, N17H hCT, Y12L hCT and DM hCT, through classical molecular dynamics (MD) simulations. Our study reveals that sCT is the least aggregation prone derivative, and the double mutation at position 12 and 17 can reduce the aggregation propensity of this peptide. Also, we have applied these mutant variants of hCT as peptide inhibitors in the self-aggregation of hCT. This study could help in understanding and preparing peptide-based inhibitors for hCT fibrillation and their applications as therapeutic drugs.

Molecular Insight into the Effects of Enhanced Hydrophobicity on Amyloid-like Aggregation.

Generally, hydrophobic amino acids provide hydrophobic interactions during peptide aggregation. However, besides the hydrophobic amino acids, some hydrophilic amino acids, such as glutamine, are also considered to be essential elements in many self-aggregating peptides. For example, huntingtin contains polyglutamine at its N-terminus and the yeast prion Sup35 protein has the GNNQQNY sequence, a peptide well-known for its ability for amyloid fibril formation. However, despite the frequent emergence of glutamine in self-assembling systems, the molecular mechanism of amyloid formation involving this unique amino acid has not been well documented. It is still not clear how this hydrophilic amino acid is responsible for the hydrophobic interaction in the self-association process. Therefore, in this study, we have carried out classical molecular dynamics simulations of the GNNQQNY peptide and its derivatives in pure water. We quantify the propensity for the formation of ß-sheet conformation with an increasing glutamine number in the peptide sequence. In addition, we assess the importance of the hydrophobicity of the dimethanediyl group present in glutamine (as well as in glutamic acid) for the self-association of the peptides through nonpolar solvent medium simulations.

In silico study of osmolytic effects of choline-O-sulfate on urea induced unfolding of Trp-cage mini-protein: An atomistic view from replica exchange molecular dynamics simulation.

The event of protein folding is associated with essential biological functionalities and unfolding of protein native state can cause intra-cellular toxicity leading to biological dysfunctions and even cell death. The present study discusses the folding-unfolding equilibrium of the small globular protein Trp-cage in presence of denaturing and protecting osmolytes urea and choline-O-sulfate (COS), respectively, employing Replica Exchange Molecular Dynamics (REMD), extensive free energy calculations and temperature scanned free energy landscapes. It is shown that, while 6 M urea quite easily denatures the protein, 0.5 M and 1 M COS is able to protect the protein from urea induced denaturation at room temperature. However, REMD simulations reveal that while the protein in pure water can withstand a simulation temperature as high as 420 K without melting, the protecting effect of 0.5 M and 1 M COS is operative up to 300 and 340 K respectively. This study furnishes evidences to shed light into the protecting mechanism of COS regarding urea induced protein unfolding, thereby putting forward the use of COS as a proper protecting osmolyte towards different types of proteins.

The conformational stability of terminal helices of λ-repressor protein in aqueous dodine and choline-O-sulfate solutions.

In this article, we have ventured into the denaturation of fast folding λ6-85-repressor protein at a millimolar concentration of dodine and henceforth, evaluated the candidature of choline-O-sulfate as a protecting osmolyte against it, employing classical molecular dynamics simulations. Our simulation results show that, the terminal helices of λ-repressor protein get unfolded in presence of ∼15 mM dodine while 0.5 M and higher concentration of COS can prevent this deleterious effect of dodine. Careful analyses of a set of simulations with increasing COS concentration reveals that a higher concentration of COS can provide remarkable stability to the protein, even slightly better than its native state in water. Different interaction parameters show that in aqueous dodine, both the dodinium and acetate ions interact strongly with the terminal helices to disrupt the structure whereas in presence of COS, due to the preferential interaction of COS with the protein molecule, dodine molecules get excluded from the protein surface. In addition, the favorable interaction of COS with dodinium head group, the dodinium ions become less available to the vicinity of protein surface which also plays an indirect but decisive role to prevent the unfolding of the terminal helical domains of the λ-repressor protein.

Molecular dynamics simulation study on the inhibitory effects of choline-O-sulfate on hIAPP protofibrilation.

Type 2 diabetes mellitus (T2Dm) is a neurodegenerative disease, which occurs due to the self-association of human islet amyloid polypeptide (hIAPP), also known as human amylin. It was reported experimentally that choline-O-sulfate (COS), a small organic molecule having a tertiary amino group and sulfate group, can prevent the aggregation of human amylin without providing the mechanism of the action of COS in the inhibition process. In this work, we investigate the influence of COS on the full-length hIAPP peptide by performing 500 ns classical molecular dynamics simulations. From pure water simulation (without COS), we have identified the residues 11-20 and 23-36 that mainly participate in the fibril formation, but in the presence of 1.07 M COS these residues become totally free of ß-sheet conformation. Our results also show that the sulfate oxygen of COS directly interacts with the peptide backbone, which leads to the local disruption of peptide-peptide interaction. Moreover, the presence of favorable peptide-COS vdW interaction energy and high coordination number of COS molecules in the first solvation shell of the peptide indicates the hydrophobic solvation of the peptide residues by COS molecules, which also play a crucial role in the prevention of ß-sheet formation. Finally, from the potential of mean force (PMFs) calculations, we observe that the free energy between two peptides is more negative in the absence of COS and with increasing concentration of COS, it becomes unfavorable significantly indicating that the peptide dimer formation is most stable in pure water, which becomes less favorable in the presence of COS. © 2019 Wiley Periodicals, Inc.

Inhibitory Effect of Choline- O-sulfate on Aß16-22 Peptide Aggregation: A Molecular Dynamics Simulation Study.

The aggregation of Aß16-22 peptide, the smallest fragment of full-length Aß1-42 with seven residues, plays a very crucial role in Aß toxicity, hence causing Alzheimer's disease. Alzheimer's disease (AD) is a progressive neurodegenerative disease associated with brain disorder, and currently there is no treatment available in the market to cure it permanently. So, drug design for the curable treatment of AD is a very challenging problem. In this study, we have investigated the inhibitory effect of choline- O-sulfate (COS) in the oligomerization of Aß16-22 peptide. We have carried out a series of classical simulations using two different types of force field parameters, namely, CGenFF and GAFF and found that this small seven residue peptide aggregates in pure water to form fibrils but in the presence of the inhibitor COS, the formation of ß-sheet structure is prevented. Residue-wise secondary structure analysis shows that the hydrophobic core of the peptide LVFFA contains high percentage of ordered ß-sheet conformation in pure water which becomes negligible with the addition of COS. Different types of interaction energies, radial distribution functions, coordination number calculation, and hydrogen bond analysis show that COS interacts with the peptide backbone nitrogen through hydrogen bonding as well as the solvation of peptide hydrophobic residues by it, playing a major role to prevent the peptide aggregation in water. It is worth mentioning that the results obtained from both of the force field parameters draw very similar conclusions. In this work, we have also shown that COS can disaggregate the preformed five-stranded protofibril of Aß16-22 at a concentration of 0.95 M.

How Does Aqueous Choline- O-Sulfate Solution Nullify the Action of Urea in Protein Denaturation?

Choline- O-sulfate (COS) acts as a protecting osmolyte in several plants, fungal, and bacterial species. Classical molecular dynamics simulation is performed to examine the molecular mechanism by which COS molecules counteract urea-conferred denaturation of the S-peptide analogue. The calculations of root mean square deviation, the radius of gyration of the Cα atom, and the solvent accessible surface area of the peptide heavy atoms imply that the 4-12 residues of the peptide in pure water remain in helical conformation at 310 K temperature. But, in binary ∼8 M aqueous urea solution the peptide loses its native conformation. Interestingly, in the ternary peptide-urea-COS system with 0.30 M COS concentration, the native conformation of the peptide remains preserved. The estimation of the average number of hydrogen bonds between different solution species indicates that it is the preferential urea-COS interactions, which influence peptide-urea interactions significantly. This observation is further confirmed by the calculation of atomic density map of urea around the peptide heavy atoms and time-averaged relative local distribution functions involving peptide and urea. Moreover, the exclusion of COS molecules from the peptide surface is also confirmed by the determination of the number of COS molecules in the first solvation shell of the peptide as well as from the calculated time-averaged relative local distribution functions involving peptide and COS. A sharp drop in the diffusion coefficient values of all solution species is observed as COS is added. These findings suggest that it is the preferential solvation of urea molecule by COS, which makes the former (urea) less available for the peptide to show its deleterious effect and hence the native conformation of the peptide is retained.