CD38-RyR2 axis-mediated signaling impedes CD8+ T cell response to anti-PD1 therapy in cancer.

PD1 blockade therapy, harnessing the cytotoxic potential of CD8+ T cells, has yielded clinical success in treating malignancies. However, its efficacy is often limited due to the progressive differentiation of intratumoral CD8+ T cells into a hypofunctional state known as terminal exhaustion. Despite identifying CD8+ T cell subsets associated with immunotherapy resistance, the molecular pathway triggering the resistance remains elusive. Given the clear association of CD38 with CD8+ T cell subsets resistant to anti-PD1 therapy, we investigated its role in inducing resistance. Phenotypic and functional characterization, along with single-cell RNA sequencing analysis of both in vitro chronically stimulated and intratumoral CD8+ T cells, revealed that CD38-expressing CD8+ T cells are terminally exhausted. Exploring the molecular mechanism, we found that CD38 expression was crucial in promoting terminal differentiation of CD8+ T cells by suppressing TCF1 expression, thereby rendering them unresponsive to anti-PD1 therapy. Genetic ablation of CD38 in tumor-reactive CD8+ T cells restored TCF1 levels and improved the responsiveness to anti-PD1 therapy in mice. Mechanistically, CD38 expression on exhausted CD8+ T cells elevated intracellular Ca2+ levels through RyR2 calcium channel activation. This, in turn, promoted chronic AKT activation, leading to TCF1 loss. Knockdown of RyR2 or inhibition of AKT in CD8+ T cells maintained TCF1 levels, induced a sustained anti-tumor response, and enhanced responsiveness to anti-PD1 therapy. Thus, targeting CD38 represents a potential strategy to improve the efficacy of anti-PD1 treatment in cancer.

Microbiome Metabolome Integration Platform (MMIP): a web-based platform for microbiome and metabolome data integration and feature identification.

A microbial community maintains its ecological dynamics via metabolite crosstalk. Hence, knowledge of the metabolome, alongside its populace, would help us understand the functionality of a community and also predict how it will change in atypical conditions. Methods that employ low-cost metagenomic sequencing data can predict the metabolic potential of a community, that is, its ability to produce or utilize specific metabolites. These, in turn, can potentially serve as markers of biochemical pathways that are associated with different communities. We developed MMIP (Microbiome Metabolome Integration Platform), a web-based analytical and predictive tool that can be used to compare the taxonomic content, diversity variation and the metabolic potential between two sets of microbial communities from targeted amplicon sequencing data. MMIP is capable of highlighting statistically significant taxonomic, enzymatic and metabolic attributes as well as learning-based features associated with one group in comparison with another. Furthermore, MMIP can predict linkages among species or groups of microbes in the community, specific enzyme profiles, compounds or metabolites associated with such a group of organisms. With MMIP, we aim to provide a user-friendly, online web server for performing key microbiome-associated analyses of targeted amplicon sequencing data, predicting metabolite signature, and using learning-based linkage analysis, without the need for initial metabolomic analysis, and thereby helping in hypothesis generation.

Exploring Cyclic Peptide Nanotube Stability Across Diverse Lipid Bilayers and Unveiling Water Transport Dynamics.

Cyclic Peptide Nanotubes (CPNTs) have emerged as compelling candidates for various applications, particularly as nanochannels within lipid bilayers. In this study, the stability of two CPNTs, namely 8 × [(Cys-Gly-Met-Gly)2] and 8 × [(Gly-Leu)4], are comprehensively investigated across different lipid bilayers, including 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), a mixed model membrane (POPE/POPG), and a realistic yeast model membrane. The results demonstrate that both CPNTs maintain their tubular structures in all lipid bilayers, with [(Cys-Gly-Met-Gly)2] showing increased stability over an extended period in these lipid membranes. The insertion of CPNTs shows negligible impact on lipid bilayer properties, including area per lipid, volume per lipid, and bilayer thickness. The study demonstrates that the CPNT preserves its two-line water movement pattern within all the lipid membranes, reaffirming their potential as water channels. The MSD curves further reveal that the dynamics of water molecules inside the nanotube are similar for all the bilayer systems with minor differences that arise due to different lipid environments.

Influence of salt and temperature on the self-assembly of cyclic peptides in water: a molecular dynamics study.

It is found in the literature that cyclic peptides (CPs) are able to self-assemble in water to form cyclic peptide nanotubes (CPNTs) and are used extensively in the field of nanotechnology. Several factors influence the formation and stability of these nanotubes in water. However, an extensive study of the contribution of several important factors is still lacking. The purpose of this study is to explore the effect of temperature and salt (NaCl) on the association tendency of CPs. Furthermore, the self-association behavior of CPs in aqueous solutions at various temperatures is also thoroughly discussed. Cyclo-[(Asp-D-Leu-Lys-D-Leu)2] is considered for this study and a series of classical molecular dynamics (MD) simulations at three different temperatures, viz. 280 K, 300 K, and 320 K, both in pure water and in NaCl solutions of different concentrations are carried out. The calculations of radial distribution functions, preferential interaction parameters, cluster formation and hydrogen bonding properties suggest a strong influence of NaCl concentration on the association propensity of CPs. Low NaCl concentration hinders CP association while high NaCl concentration facilitates the association of CPs. Besides this, the association of CPs is found to be enhanced at low temperature. Furthermore, the thermodynamics of CP association is predominantly found to be enthalpy driven in both the presence and absence of salt. No crossover between enthalpy and entropy in CP association is observed. In addition, the MM-GBSA method is used to investigate the binding free energies of the CP rings that self-assembled to form nanotube like structures at all three temperatures.

Nested DWT-Based CNN Architecture for Monocular Depth Estimation.

Applications such as medical diagnosis, navigation, robotics, etc., require 3D images. Recently, deep learning networks have been extensively applied to estimate depth. Depth prediction from 2D images poses a problem that is both ill-posed and non-linear. Such networks are computationally and time-wise expensive as they have dense configurations. Further, the network performance depends on the trained model configuration, the loss functions used, and the dataset applied for training. We propose a moderately dense encoder-decoder network based on discrete wavelet decomposition and trainable coefficients (LL, LH, HL, HH). Our Nested Wavelet-Net (NDWTN) preserves the high-frequency information that is otherwise lost during the downsampling process in the encoder. Furthermore, we study the effect of activation functions, batch normalization, convolution layers, skip, etc., in our models. The network is trained with NYU datasets. Our network trains faster with good results.

Sequestration of eIF4A by angiomotin: A novel mechanism to restrict global protein synthesis in trophoblast cells.

Enrichment of angiomotin (AMOT) in the ectoplacental cone of E7.5 murine placenta prompted our investigation on the role of AMOT in trophoblast differentiation. We show here that AMOT levels increased in mouse placenta during gestation and also upon induction of differentiation in trophoblast stem cell ex vivo. Proteomic data unravelling AMOT-interactome in trophoblast cells indicated a majority of AMOT interactors to be involved in protein translation. In-depth analysis of AMOT-interactome led to identification of eukaryotic translation initiation factor 4A (eIF4A) as the most plausible AMOT interactor. Loss of function of AMOT enhanced, whereas, gain in function resulted in decline of global protein synthesis in trophoblast cells. Bioinformatics analysis evaluating the potential energy of AMOT-eIF4A binding suggested a strong AMOT-eIF4A interaction using a distinct groove encompassing amino acid residue positions 238 to 255 of AMOT. Co-immunoprecipitation of AMOT with eIF4A reaffirmed AMOT-eIF4A association in trophoblast cells. Deletion of 238 to 255 amino acids of AMOT resulted in abrogation of AMOT-eIF4A interaction. In addition, 238 to 255 amino acid deletion of AMOT was ineffective in eliciting AMOT's function in reducing global protein synthesis. Interestingly, AMOT-dependent sequestration of eIF4A dampened its loading to the m7 -GTP cap and hindered its interaction with eIF4G. Furthermore, enhanced AMOT expression in placenta was associated with intrauterine growth restriction in both rats and humans. These results not only highlight a hitherto unknown novel function of AMOT in trophoblast cells but also have broad biological implications as AMOT might be an inbuilt switch to check protein synthesis in developmentally indispensable trophoblast cells.

Phenylpropanoids on the Inhibition of ß-Amyloid Aggregation and the Movement of These Molecules through the POPC Lipid Bilayer.

Alzheimer's disease (AD), caused by Aß aggregation, is a major concern in medical research. It is a neurodegenerative disorder, leading to a loss of cognitive abilities, which is still claiming the lives of many people all over the world. This poses a challenge before the scientific community to discover effective drugs which can prevent such toxic aggregation. Recent experimental findings suggest the potency of two naturally-occurring phenylpropanoids, Schizotenuin A (SCH) and Lycopic Acid B (LAB) which can effectively combat the deleterious effects of Aß aggregation, although nothing is known about their mechanism of inhibition. In this work, we deal with an extensive computational study on the inhibitory effects of these inhibitors by using an all-atom molecular dynamics simulation to interpret the underlying mechanism of their inhibitory processes. A series of investigations is carried out while studying the various structural and conformational changes of the peptide chains in the absence and presence of inhibitors. To investigate the details of the interactions between the peptide residues and inhibitors, nonbonding energy calculations, the radial distribution function, the coordination number of water and inhibitor molecules around the peptide residues, and hydrogen-bonding interactions are calculated. The potential of mean force (PMF) is calculated to estimate aggregate formation from their free-energy profiles. It is seen that the hydrophobic core of the KLVFFAE undergoes aggregation and that these inhibitors show great promise in preventing the onset of AD in the future by preventing Aß aggregation. Also, the translocation studies on these inhibitors through a model POPC lipid bilayer shed light on their permeation properties and biocompatibility.

Inhibition of Aß16-22 Peptide Aggregation by Small Molecules and Their Permeation through POPC Lipid Bilayer: Insight from Molecular Dynamics Simulation Study.

Alzheimer's Disease is a rapidly progressing irreversible neurodegenerative disorder characterized by neuronal cell deterioration that endangers human health. With its proper therapeutic treatment being unavailable, several research groups throughout the world are involved in designing efficient drug molecules. However, the elusive mechanism of action of the drugs as well as their debilitating side effects pose major challenges in this regard. In the present article, we investigated the inhibitory effect of an indanone-carbamate-based molecule on Aß16-22 peptide aggregation by employing a series of all-atom molecular dynamics simulation study. To gain explicit insights, we studied the role of inhibitor molecules on the disruption of highly arranged ß-sheet of peptides by various types of analyses such as structural analysis, Cα-Cα-atom distance, residue-wise contact map, and solvent accessible surface area. The results obtained from various analyses revealed that the inhibitor molecules interacted with Aß16-22 peptides to destabilize its arranged ß-sheet conformer via hydrophobic interaction. To further comprehend the effect of inhibitors on amyloid aggregation, we also determined interaction energy, hydration number, radial distribution function, hydrogen bonding, and potential of mean forces. In addition, the permeability of the inhibitors through model POPC lipid bilayer via passive diffusion was also analyzed. Our study is noteworthy in that it elucidates the strong interaction between inhibitors and the central hydrophobic core of peptides comprising aromatic phenylalanine residues, as well as the passive translocation of inhibitors across POPC lipid bilayers.

The chaotropic effect of ions on the self-aggregating propensity of Whitlock's molecular tweezers.

Molecular tweezers feature the first class of artificial receptors to pique the interest of researchers and emerge as an effective therapeutic candidate. The exceptional structure and exquisite binding specificity of tweezers establish this overall class of receptors as a promising tool, with abundant applications. However, their inclination to self-aggregate by mutual π-π stacking interactions of their aromatic arms diminishes their efficacy as a therapeutic candidate. Therefore, following up on sporadic studies, since the discovery of the Hofmeister series, on the ability of ions to either solvate (salting-in) or induce aggregation (salting-out) of hydrophobic solutes, the notions of ion-specificity effects are utilized on tweezer moieties. The impacts of three different aluminum salts bearing anions Cl-, ClO4- and SCN- on the self-association propensity of Whitlock's caffeine-pincered molecular tweezers are investigated, with a specific emphasis placed on elucidating the varied behavior of the ions on the hydration ability of tweezers. The comparative investigation is conducted employing a series of all-atom molecular dynamics simulations of five tweezer molecules in pure water and three salt solutions, at two different concentrations each, maintaining a temperature of 300 K and a pressure of 1 atm, respectively. Radial distribution functions, coordination numbers, and SASA calculations display a steady reduction in the aggregation proclivity of the receptor molecules with an increase in salt concentration, as progressed along the Hofmeister series. Orientational preferences between the tweezer arms reveal a disruptive effect in the regular π-π stacking interactions, in the presence of high concentrations of ClO4- and SCN- ions, while preferential interactions and tetrahedral order parameters unveil the underlying mechanism, by which the anions alter the solubility of the hydrophobic molecules. Overall, it is observed that SCN- exhibits the highest salting-in effect, followed by ClO4-, with both anions inhibiting tweezer aggregation through different mechanisms. ClO4- ions impart an effect by moderately interacting with the solute molecules as well as modifying the water structure of the bulk solution promoting solvation, whereas, SCN- ions engage entirely in interaction with specific tweezer sites. Cl- being the most charge-dense of the three anionic species experiences stronger hydration and therefore, imparts a very negligible salting-in effect.

Appraising the potency of small molecule inhibitors and their graphene surface-mediated organizational attributes on uric acid-melamine clusters.

Uric acid (UA) and melamine (MM) crystallization in humans is associated with adverse medical conditions, including the germination of kidney stones, because of their low solubility. The growth of kidney stones, usually formed on renal papillary facades, is accomplished on the matrix-coated surface by the aggregation of preformed crystals or secondary crystal nucleation. Therefore, the effects of inhibitors such as theobromine (TB) and allopurinol (AP) on MM-UA aggregation are investigated by employing classical molecular dynamics simulations on a graphene surface. This impersonates the exact essence of the precipitation of kidney stones. The interaction between MM-UA is very intense and, thus, large clusters are formed on the surface. The presence of TB and AP will, however, substantially inhibit their aggregation. TB and AP significantly impede UA aggregation in particular. Therefore, lower order UA clusters are formed. These smaller UA clusters then pull a lower number of MM towards themselves, resulting in a smaller order UA-MM cluster. MM and UA aggregation on a 2D graphene surface is found to be spontaneous. There is no difference in these molecules' adsorption with a change in the force field parameters (i.e., GAFF and OPLS-AA) for graphene. Moreover, the greater the surface area of graphene, the more molecules are absorbed. The solute-surface van der Waals interaction energy plays a driving force in the adsorption of solute molecules on the surface. In addition, interactions like hydrogen bonding and π-stacking over the graphene surface involve binding all like molecules. These aggregated solute molecules strongly attract more like molecules until all solute molecules are adsorbed on the graphene surface, as estimated by enhanced sampling. The molecular origin of graphene exfoliation by MM is also described here. The present work helps to design novel kidney stone inhibitors.

Nature and Dimensions of Systemic Hyperinflammation and its Attenuation by Convalescent Plasma in Severe COVID-19.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing coronavirus disease 2019 (COVID-19), has led to significant morbidity and mortality. While most suffer from mild symptoms, some patients progress to severe disease with acute respiratory distress syndrome (ARDS) and associated systemic hyperinflammation. METHODS: First, to characterize key cytokines and their dynamics in this hyperinflammatory condition, we assessed abundance and correlative expression of a panel of 48 cytokines in patients progressing to ARDS as compared to patients with mild disease. Then, in an ongoing randomized controlled trial of convalescent plasma therapy (CPT), we analyzed rapid effects of CPT on the systemic cytokine dynamics as a correlate for the level of hypoxia experienced by the patients. RESULTS: We identified an anti-inflammatory role of CPT independent of its neutralizing antibody content. CONCLUSIONS: Neutralizing antibodies, as well as reductions in circulating interleukin-6 and interferon-γ-inducible protein 10, contributed to marked rapid reductions in hypoxia in response to CPT. CLINICAL TRIAL REGISTRY OF INDIA: CTRI/2020/05/025209. http://www.ctri.nic.in/.

Underlying Mechanisms of Allopurinol in Eliminating Renal Toxicity Induced by Melamine-Uric Acid Complex Formation: A Computational Study.

Using molecular dynamics, we address uric acid (UA) replacement by a model small-molecule inhibitor, allopurinol (AP), from its aggregated cluster in a columnar fashion. Experimentally it has been affirmed that AP is efficient in preventing UA-mediated renal stone formation. However, no study has presented the underlying mechanisms yet. Hence, a theoretical approach is presented for mapping the AP, which binds to melamine (MM) and UA clusters. In AP's presence, the higher-order cluster of UA molecules turns into a lower-order cluster, which "drags" fewer MM to them. Consequently, the MM-UA composite structure gets reduced. It is worth noting that UA-AP and AP-MM hydrogen-bonding interactions often play an essential role in reducing the UA-MM cluster size. Interestingly, an AP around UA makes a pillar-like structure, confirmed by defining the point-plane distribution function. The decomposition of the preferential interaction by Kirkwood-Buff integral into different angles like 0°-30°, 30°-60°, and 60°-90° firmly establishes the phenomenon mentioned above. However, the structural order for such π-stacking interactions between AP and UA molecules is not hierarchical but rather more spontaneous. The driving force behind UA-AP-MM composite formation is the favorable complexation energy that can be inferred by computing pairwise binding free energies for all possible combinations. Performing enhanced sampling and quantum calculations further confirms the evidence for UA degradation.

Translocation of Endo-Functionalized Molecular Tubes across Different Lipid Bilayers: Atomistic Molecular Dynamics Simulation Study.

Various artificial receptors, such as calixarenes, cyclodextrins, cucurbit[n]urils, and their acyclic compounds, pliiar[n]arenes, deep cavitands, and molecular tweezers, can permeate the lipid membranes and they are used as drug carriers to improve the drug solubility, stability, and bioavailability. Inspired by these, we have employed atomistic molecular dynamics simulation to examine the effects of endo-functionalized molecular tubes or naphthotubes (host-1a and host-1b) on seven different types of model lipid bilayers and the permeation properties of these receptors through these model lipid bilayers. Lipid types include six model lipid bilayers (POPC, POPE, DOPC, POPG, DPPE, POPE/POPG) and one realistic membrane (Yeast). We observe that these receptors are spontaneously translocated toward these model lipid bilayer head regions and do not proceed further into these lipid bilayer tail regions (reside at the interface between lipid head and lipid tail region), except for the DPPE-containing systems. In the DPPE model lipid bilayer-containing systems (1a-dppe and 1b-dppe), receptor molecules are only adsorbed on the bilayer surface and reside at the interface between lipid head and water. This finding is also supported by the biased free-energy profiles of these translocation processes. Passive transport of these receptors may be possible through these model lipid bilayers (due to low barrier height), except for DPPE bilayer-containing systems (that have a very high energy barrier at the center). The results from these simulations provide insight into the biocompatibility of host-1a or host-1b in microscopic detail. Based on this work, more research is needed to fully comprehend the role of these synthesized receptors as a prospective drug carrier.

Role of Hydrotropes in Sparingly Soluble Drug Solubilization: Insight from a Molecular Dynamics Simulation and Experimental Perspectives.

Drug molecules' therapeutic efficacy depends on their bioavailability and solubility. But more than 70% of the formulated drug molecules show limited effectiveness due to low water solubility. Thus, the water solubility enhancement technique of drug molecules becomes the need of time. One such way is hydrotropy. The solubilizing agent of a hydrophobic molecule is generally referred to as a hydrotrope, and this phenomenon is termed hydrotropy. This method has high industrial demand, as hydrotropes are noninflammable, readily available, environmentally friendly, quickly recovered, cost-effective, and not involved in solid emulsification. The endless importance of hydrotropes in industry (especially in the pharmaceutical industry) motivated us to prepare a feature article with a clear introduction, detailed mechanistic insights into the hydrotropic solubilization of drug molecules, applications in pharma industries, and some future directions of this technique. Thus, we believe that this feature article will become an adequate manual for the pharmaceutical researchers who want to explore all of the past perspectives of the hydrotropic action of hydrotropes in pharmaceutics.

An in silico investigation of the binding modes and pathway of APTO-253 on c-KIT G-quadruplex DNA.

The stability of c-KIT G-quadruplex DNA via ligands has been a significant concern in the growing field of cancer therapy. Thus, it is very important to understand the mechanism behind the high binding affinity of the small drug molecules on the c-KIT G-quadruplex DNA. In this study, we have investigated the binding mode and pathway of the APTO-253 ligand on the c-KIT G-quadruplex DNA employing a total of 10 µs all atom molecular dynamics simulations and further 8.82 µs simulations via the umbrella sampling method using both OL15 and BSC1 latest force fields for DNA structures. From the cluster structure analysis, mainly three binding pathways i.e., top, bottom and side loop stacking modes are identified. Moreover, RMSD, RMSF and 2D-RMSD values indicate that the c-KIT G-quadruplex DNA and APTO-253 molecules are stable throughout the simulation run. Furthermore, the number of hydrogen bonds in each tetrad and the distance between the two central K+ cations confirm that the c-KIT G-quadruplex DNA maintains its conformation in the process of complex formation with the APTO-253 ligand. The binding free energies and the minimum values in the potential of mean forces suggest that the binding processes are energetically favorable. Furthermore, we have found that the bottom stacking mode is the most favorable binding mode among all the three modes for the OL15 force field. However, for the BSC1 force field, both the top and bottom binding modes of the APTO-253 ligand in c-KIT G-quadruplex DNA are comparable to each other. To investigate the driving force for the complex formation, we have noticed that the van der Waals (vdW) and π-π stacking interactions are mainly responsible. Our detailed studies provide useful information for the discovery of novel drugs in the field of stabilization of G-quadruplex DNAs.

Theoretical investigation of conformational deviation of the human parallel telomeric G-quadruplex DNA in the presence of different salt concentrations and temperatures under confinement.

Various experimental reports address the stability of G-quadruplex DNA inside a close confinement such as α-hemolysin, nanocavity water pool and different metal-organic-frameworks (MOFs). To understand the conformational change of G-quadruplex DNA at the atomistic level, we have carried out a total of 40 µs simulation run under both non-polar and polar confinement conditions. To investigate the dynamics, we have considered two different KCl salt concentrations, i.e., 0.47 M (minimal salt concentration) and higher than 2 M (higher salt concentration), at two distinct temperatures, 300 K and 350 K. Here, we have observed that the human telomeric G-quadruplex DNA deviates more from its crystal structure at minimal salt concentration under both non-polar and polar confinement conditions. Besides, the loop regions deviate and fluctuate more compared to the other regions, i.e., sugar-phosphate backbone and tetrad regions. The presence of K+ ions is found to be primarily responsible for this phenomenon. From the spatial density function (SDF) plots, a higher density of K+ ions is observed in the backbone region. Furthermore, from the residue-wise first solvation shell estimation, we have noticed that the K+ ions mainly accumulate in the tetrad region under both non-polar and polar confinement conditions due to which the tetrad regions are more rigid than the loop regions. Higher salt concentration results in increased rigidity of the G-quadruplex DNA. Our study provides valuable insight into the conformational deviation of the G-quadruplex DNA under nanoconfinement conditions.

Exploration on the drug solubility enhancement in aqueous medium with the help of endo-functionalized molecular tubes: a computational approach.

One major problem in the pharmaceutical industry is the aqueous solubility of newly developed orally administered drug candidates. More than 50% of newly developed drug molecules suffer from low aqueous solubility. The therapeutic effects of drug molecules are majorly dependent on the bioavailability and, in essence, on the solubility of the used drug molecules. Thus, enhancement of drug solubility of sparingly soluble drug molecules is a need of modern times. Considering the high importance of drug solubility, we have computationally shown the enhancement of drug solubility for seven class II (poorly water-soluble) drug molecules in a water medium. The uses of supramolecular macrocycles have immense importance in the same field. Thus, we have used two synthetic supramolecular receptors named host-1a and host-1b to enhance the water solubility of fluorouracil, albendazole, camptothecin, clopidogrel, indomethacin, melphalan, and tolfenamic acid drug molecules. Biomedical engagements of a supramolecular receptor commence with the formation of stable host-drug complexes. These complexations enhance the water solubility of drug molecules and sustain the release rate and bioavailability of drug molecules. Thus, in this work, we focus on the formation of stable host-drug complexes in water medium. Molecular dynamics simulation is applied to analyze the structural features and the energetics involved in the host-drug complexation process. The information obtained at the atomistic level helps us gain better insights into the key interactions that operate to produce such highly stable complexes. Thus, we can propose that these two supramolecular receptors may be used as drug solubilizing agents, and patients will benefit from this theragnostic application shortly.

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 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.

The miscibility and solubility of uric acid and vitamin C in the solution phase and their structural alignment in the solid-liquid interface.

The crystallization of uric acid (UA) in humans is correlated with unpropitious medical predicaments, including gout and kidney stone germination. Its comparatively low solubility in physiological solutions is a significant contributory factor to UA biomineralization. The inhibition of UA aggregation is investigated as a reasonable approach for reducing kidney and gout-related problems. Therefore, we examine the role of vitamin C (Vit-C), a water-soluble vitamin, in the aggregation of UA, and its potency in solubilizing UA has been confirmed experimentally. We notice that Vit-C encapsulates the aggregated UA. Moreover, it can dismantle the assemblies of UA. We have proffered comprehensive molecular mechanisms of the interplay between the aggregated UA and Vit-C. Vit-C molecules are interspersed in solution due to its non-aggregating nature. We perceive that, through hydrogen bonding and aromatic stacking interactions, Vit-C molecules interact with UA molecules. The determination of the Flory-Huggins interaction parameters suggests that the presence of Vit-C enhances the solubility of UA aggregates. In addition, UA molecules are conformed on a monolayer graphene sheet, where they are assembled to create a 2D self-assembly. Vit-C, however, encapsulates and disseminates itself within the aggregated UA molecules on the surface. Therefore, the molecular mechanisms of the impact of Vit-C on UA aggregation can provide relevant insights into drug design against chronic diseases.