Evaluating Single-Nucleotide Polymorphisms in Inflammasome Proteins and Serum Levels of IL-18 and IL-1ß in Kidney Interstitial Damage in Anti-Neutrophilic Cytoplasmic Antibody-Associated Vasculitis.

The inflammasome regulates the innate inflammatory response and is involved in autoimmune diseases. In this study, we explored the levels of IL-18 and IL-1ß in serum and urine and the influence of various single-nucleotide polymorphisms (SNPs) on kidney lesions at diagnosis in patients with ANCA-associated vasculitis (AAV) and their clinical outcomes. Ninety-two patients with renal AAV were recruited, and blood and urine were collected at diagnosis. Serum and urine cytokine levels were measured by ELISA. DNA was extracted and genotyped using TaqMan assays for SNPs in several inflammasome genes. Lower serum IL-18 (p = 0.049) and the IL-18 rs187238 G-carrier genotype (p = 0.042) were associated with severe fibrosis. The IL-18 rs1946518 TT genotype was associated with an increased risk of relapse (p = 0.05), whereas GG was related to better renal outcomes (p = 0.031). The rs187238 GG genotype was identified as a risk factor for mortality within the first year after AAV diagnosis, independent of the requirement for dialysis or lung involvement (p = 0.013). We suggest that decreased cytokine levels could be a surrogate marker of scarring and chronicity of the renal lesions, together with the rs187238 GG genotype. If our results are validated, the rs1946518 TT genotype predicts the risk of relapse and renal outcomes during follow-up.

Advances in Functionalization of Bioresorbable Nanomembranes and Nanoparticles for Their Use in Biomedicine.

Bioresorbable nanomembranes (NMs) and nanoparticles (NPs) are powerful polymeric materials playing an important role in biomedicine, as they can effectively reduce infections and inflammatory clinical patient conditions due to their high biocompatibility, ability to physically interact with biomolecules, large surface area, and low toxicity. In this review, the most common bioabsorbable materials such as those belonging to natural polymers and proteins for the manufacture of NMs and NPs are reviewed. In addition to biocompatibility and bioresorption, current methodology on surface functionalization is also revisited and the most recent applications are highlighted. Considering the most recent use in the field of biosensors, tethered lipid bilayers, drug delivery, wound dressing, skin regeneration, targeted chemotherapy and imaging/diagnostics, functionalized NMs and NPs have become one of the main pillars of modern biomedical applications.

IgG1-b12-HIV-gp120 Interface in Solution: A Computational Study.

The use of broadly neutralizing antibodies against human immunodeficiency virus type 1 (HIV-1) has been shown to be a promising therapeutic modality in the prevention of HIV infection. Understanding the b12-gp120 binding mechanism under physiological conditions may assist the development of more broadly effective antibodies. In this work, the main conformations and interactions between the receptor-binding domain (RBD) of spike glycoprotein gp120 of HIV-1 and the IgG1-b12 mAb are studied. Accelerated molecular dynamics (aMD) and ab initio hybrid molecular dynamics have been combined to determine the most persistent interactions between the most populated conformations of the antibody-antigen complex under physiological conditions. The results show the most persistent receptor-binding mapping in the conformations of the antibody-antigen interface in solution. The binding-free-energy decomposition reveals a small enhancement in the contribution played by the CDR-H3 region to the b12-gp120 interface compared to the crystal structure.

Computer simulations on oxidative stress-induced reactions in SARS-CoV-2 spike glycoprotein: a multi-scale approach.

Oxidative stress, which occurs when an organism is exposed to an adverse stimulus that results in a misbalance of antioxidant and pro-oxidants species, is the common denominator of diseases considered as a risk factor for SARS-CoV-2 lethality. Indeed, reactive oxygen species caused by oxidative stress have been related to many virus pathogenicity. In this work, simulations have been performed on the receptor binding domain of SARS-CoV-2 spike glycoprotein to study what residues are more susceptible to be attacked by ·OH, which is one of the most reactive radicals associated to oxidative stress. The results indicate that isoleucine (ILE) probably plays a crucial role in modification processes driven by radicals. Accordingly, QM/MM-MD simulations have been conducted to study both the ·OH-mediated hydrogen abstraction of ILE residues and the induced modification of the resulting ILE radical through hydroxylation or nitrosylation reactions. All in all, in silico studies show the importance of the chemical environment triggered by oxidative stress on the modifications of the virus, which is expected to help for foreseeing the identification or development of antioxidants as therapeutic drugs.

Poly(aspartic acid) Biohydrogel as the Base of a New Hybrid Conducting Material.

In the present study, a composite made of conducting polymer, poly(3,4-ethylenedioxythiophene) (PEDOT), and a biodegradable hydrogel of poly(aspartic acid) (PASP) were electrochemically interpenetrated with poly(hydroxymethyl-3,4-ethylenedioxythiophene) (PHMeDOT) to prepare a new interpenetrated polymer network (IPN). Different cross-linker and PEDOT MPs contents, as well as different electropolymerization times, were studied to optimize the structural and electrochemical properties. The properties of the new material, being electrically conductive, biocompatible, bioactive, and biodegradable, make it suitable for possible uses in biomedical applications.

Free-Standing, Flexible Nanofeatured Polymeric Films Prepared by Spin-Coating and Anodic Polymerization as Electrodes for Supercapacitors.

Flexible and self-standing multilayered films made of nanoperforated poly(lactic acid) (PLA) layers separated by anodically polymerized poly(3,4-ethylenedioxythiophene) (PEDOT) conducting layers have been prepared and used as electrodes for supercapacitors. The influence of the external layer has been evaluated by comparing the charge storage capacity of four- and five-layered films in which the external layer is made of PEDOT (PLA/PEDOT/PLA/PEDOT) and nanoperforated PLA (PLA/PEDOT/PLA/PEDOT/PLA), respectively. In spite of the amount of conducting polymer is the same for both four- and five-layered films, they exhibit significant differences. The electrochemical response in terms of electroactivity, areal specific capacitance, stability, and coulombic efficiency was greater for the four-layered electrodes than for the five-layered ones. Furthermore, the response in terms of leakage current and self-discharge was significantly better for the former electrodes than for the latter ones.

Tethering of the IgG1 Antibody to Amorphous Silica for Immunosensor Development: A Molecular Dynamics Study.

A key factor for improving the sensitivity and performance of immunosensors based on mechanical-plasmonic methods is the orientation of the antibody proteins immobilized on the inorganic surface. Although experimental techniques fail to determine surface phenomena at the molecular level, modern simulations open the possibility for improving our understanding of protein-surface interactions. In this work, replica exchange molecular dynamics (REMD) simulations have been used to model the IgG1 protein tethered onto the amorphous silica surface by considering a united-atom model and a relatively large system (2500 nm2 surface). Additional molecular dynamics (MD) simulations have been conducted to derive an atomistic model for the amorphous silica surface using the cristobalite crystal structure as a starting point and to examine the structure of the free IgG1 antibody in the solution for comparison when immobilized. Analyses of the trajectories obtained for the tethered IgG1, which was sampled considering 32 different temperatures, have been used to define the geometry of the protein with respect to the inorganic surface. The tilt angle of the protein with respect to the surface plane increases with temperature, the most populated values being 24, 66, and 87° at the lowest (250 K), room (298 K), and the highest (380 K) temperatures. This variation indicates that the importance of protein-surface interactions decreases with increasing temperature. The influence of the surface on the structure of the antibody is very significant in the constant region, which is directly involved in the tethering process, while it is relatively unimportant for the antigen-binding fragments, which are farthest from the surface. These results are expected to contribute to the development of improved mechanical-plasmonic sensor microarrays in the near future.

Doped photo-crosslinked polyesteramide hydrogels as solid electrolytes for supercapacitors.

High-performance hydrogels play a crucial role as solid electrolytes for flexible electrochemical supercapacitors (ESCs). More specifically, all solid-state ESCs based on renewable, biodegradable and/or biocompatible hydrogels doped with inorganic salts as electrolytes are attractive not only because of their contribution to reducing resource consumption and/or the generation of electronic garbage, but also due to their potential applicability in the biomedical field. Here, computer simulations have been combined with experimental measurements to probe the outstanding capability as solid electrolytes of photo-crosslinked unsaturated polyesteramide hydrogels containing phenylalanine, butenediol and fumarate, and doped with NaCl (UPEA-Phe/NaCl). Atomistic molecular dynamics simulations have shown the influence of the hydrogel pore structure in the migration of Na+ and Cl- ions, suggesting that UPEA-Phe/NaCl hydrogels prepared without completing the photo-crosslinking reaction will exhibit better behavior as solid electrolytes. Theoretical predictions have been confirmed by potentiodynamic and galvanostatic studies on ESCs fabricated using poly(3,4-ethylenedioxythiophene) electrodes and UPEA-Phe/NaCl hydrogels, which were obtained using different times of exposure to UV radiation (i.e. 4 and 8 h for incomplete and complete photo-crosslinking reaction). Moreover, the behavior as a solid electrolyte of the UPEA-Phe/NaCl hydrogel prepared using a photo-polymerization time of 4 h has been found to be significantly superior to those exhibited by different polypeptide and polysaccharide hydrogels, which were analyzed using ESCs with identical electrodes and experimental conditions.

New Biomarkers in Acute Tubulointerstitial Nephritis: A Novel Approach to a Classic Condition.

Acute tubulointerstitial nephritis (ATIN) is an immunomediated cause of acute kidney injury. The prevalence of ATIN among the causes of acute kidney injury (AKI) is not negligible, especially those cases related to certain drugs. To date, there is a lack of reliable non-invasive diagnostic and follow-up markers. The gold standard for diagnosis is kidney biopsy, which shows a pattern of tubulointerstitial leukocyte infiltrate. The urinalysis findings can aid in the diagnosis but are no longer considered sensitive or specific. Atthe present time, there is a rising attentiveness tofinding trustworthy biomarkers of the disease, with special focus in urinary cytokines and chemokines that may reflect kidney local inflammation. Cell-based tests are of notable interest to identify the exact drug involved in hypersensitivity reactions to drugs, manifesting as ATIN. Certain single-nucleotide polymorphisms in HLA or cytokine genes may confer susceptibility to the disease according to pathophysiological basis. In this review, we aim to critically examine and summarize the available evidence on this topic.

Exploring Frequencies of Circulating Specific Th17 Cells against Myeloperoxidase and Proteinase 3 in ANCA Associated Vasculitis.

: Background: The role of the T helper 17 (Th17) cell subset in anti-neutrophil cytoplasm antibodies (ANCA) associated vasculitis (AAV) is controversial. We hypothesized that a specific Th17 response to myeloperoxidase (MPO) or proteinase 3 (PR3) is detectable in AAV patients and is different among the disease phases. METHODS: We analyzed 43 AAV patients with renal involvement (21 acute and 22 remission patients), and 12 healthy controls. Peripheral blood mononuclear cells (PBMCs) were cultured with PR3/MPO over 48 h. Thereafter, frequencies of MPO/PR3-specific Th17 cells were assessed using an enzyme-linked immunosorbent spot (ELISpot) assay. Supernatant IL-17 concentration was quantified using ELISA. Finally, specific Th17 response after depletion of T regulatory lymphocytes (T-regs) in some remission patients was compared to the non T-reg-depleted response. RESULTS: Specific Th17 cell number was higher in acute patients compared to remission (p = 0.004). Specific Th17 cell number performed well in the disease activity detection (ROC curve area under the curve (AUC) = 0.87; p = 0.0001) with an optimal cut-off of 6 spots/million. Patients above this cut-off showed higher serum creatinine (p = 0.004), C-reactive protein (CRP) (p = 0.001) and ANCA titer (p = 0.032). Supernatant IL-17 concentration was higher in acute patients compared to remission (p = 0.035) and did not normalize to healthy control levels (p = 0.01). CONCLUSIONS: A specific Th17 cell response is present in AAV patients. This response is more pronounced in the acute phase, but persists in remission.

Molecular dynamics study on the Apo- and Holo-forms of 5-lipoxygenase.

Lipoxygenases (LOXs) are nonheme iron-containing enzymes catalyzing the dioxygenation of polyunsaturated fatty acids. LOX catalytic activity depends on the presence of iron in the active site and the iron removal is also able to affect the membrane binding properties of the enzyme. Leukotrienes biosynthesis is initiated by the action of 5-LOX at the level of nuclear membrane and the mechanism of enzyme-membrane interaction is thought to involve structural flexibility and conformational changes at the level of the protein tertiary structure. In this study, we have analyzed by molecular dynamics simulations the conformational changes induced by iron removal in 5-LOX. The data indicate that the degree of enzyme flexibility is related to the presence of iron into the active site that is able to stabilize the protein increasing its rigidity. These findings provide further evidence that the conformation and the functional activity of LOXs is tuned by the presence of iron at the active site, suggesting new approaches for the design of enzyme inhibitors.

The Costimulatory Pathways and T Regulatory Cells in Ischemia-Reperfusion Injury: A Strong Arm in the Inflammatory Response?

Costimulatory molecules have been identified as crucial regulators in the inflammatory response in various immunologic disease models. These molecules are classified into four different families depending on their structure. Here, we will focus on various ischemia studies that use costimulatory molecules as a target to reduce the inherent inflammatory status. Furthermore, we will discuss the relevant role of T regulatory cells in these inflammatory mechanisms and the costimulatory pathways in which they are involved.

Self-assembly of diphenylalanine with preclick components as capping groups.

Alkyne and azide, which are commonly used in the cycloaddition reaction recognized as "click chemistry", have been used as capping groups of two engineered diphenylalanine (FF) derivatives due to their ability to form weak intermolecular interactions (i.e. dipole-π and π-π stacking). In Poc-FF-N3, alkyne and azide act as N- and C-terminal capping groups, respectively, while such positions are exchanged in N3-FF-OPrp. The self-assembly of such two synthesized peptides has been extensively studied in their "pre-click" state, considering the influence of three different factors: the peptide concentration, the polarity of the medium, and the nature of the substrate. Poc-FF-N3 assembles into microfibers that, depending on the medium and the substrate, can aggregate hierarchically in supramolecular structures with different morphologies. The most distinctive one corresponds to very stable birefringent dendritic-like microstructures, which are derived from the ordered agglomeration of microfibers. These branched supramolecular structures, which are observed under a variety of conditions, are relatively uncommon in short FF sequences. At the molecular level, Poc-FF-N3 organizes in antiparallel ß-sheets stabilized by N-HO intermolecular hydrogen bonds and re-enforced by weak interactions between the azide and alkyne groups of neighbouring molecules. In contrast, N3-FF-OPrp exhibits a very poor tendency to organize into structures with a well-defined morphology. Theoretical calculations on model complexes indicate that the tendency of the latter peptide to organize into small amorphous agglomerates is due to its poor ability to form specific intermolecular interactions in comparison with Poc-FF-N3. The implications of the weak interactions induced by the alkyne and azide groups, which strengthen peptidepeptide hydrogen bonds and π-ladders due to the stacked aromatic phenyl side groups, are discussed.

Solvent effects on the properties of hyperbranched polythiophenes.

The structural and electronic properties of all-thiophene dendrimers and dendrons in solution have been evaluated using very different theoretical approaches based on quantum mechanical (QM) and hybrid QM/molecular mechanics (MM) methodologies: (i) calculations on minimum energy conformations using an implicit solvation model in combination with density functional theory (DFT) or time-dependent DFT (TD-DFT) methods; (ii) hybrid QM/MM calculations, in which the solute and solvent molecules are represented at the DFT level as point charges, respectively, on snapshots extracted from classical molecular dynamics (MD) simulations using explicit solvent molecules, and (iii) QM/MM-MD trajectories in which the solute is described at the DFT or TD-DFT level and the explicit solvent molecules are represented using classical force-fields. Calculations have been performed in dichloromethane, tetrahydrofuran and dimethylformamide. A comparison of the results obtained using the different approaches with the available experimental data indicates that the incorporation of effects associated with both the conformational dynamics of the dendrimer and the explicit solvent molecules is strictly necessary to satisfactorily reproduce the properties of the investigated systems. Accordingly, QM/MM-MD simulations are able to capture such effects providing a reliable description of electronic properties-conformational flexibility relationships in all-Th dendrimers.

CD154-CD40 T-cell co-stimulation pathway is a key mechanism in kidney ischemia-reperfusion injury.

Ischemia-reperfusion occurs in a great many clinical settings and contributes to organ failure or dysfunction. CD154-CD40 signaling in leukocyte-endothelial cell interactions or T-cell activation facilitates tissue inflammation and injury. Here we tested a siRNA anti-CD40 in rodent warm and cold ischemia models to check the therapeutic efficacy and anti-inflammatory outcome of in vivo gene silencing. In the warm ischemia model different doses were used, resulting in clear renal function improvement and a structural renoprotective effect. Renal ischemia activated the CD40 gene and protein expression, which was inhibited by intravenous siRNA administration. CD40 gene silencing improved renal inflammatory status, as seen by the reduction of CD68 and CD3 T-cell infiltrates, attenuated pro-inflammatory, and enhanced anti-inflammatory mediators. Furthermore, siRNA administration decreased a spleen pro-inflammatory monocyte subset and reduced TNFα secretion by splenic T cells. In the cold ischemia model with syngeneic and allogeneic renal transplantation, the most effective dose induced similar functional and structural renoprotective effects. Our data show the efficacy of our siRNA in modulating both the local and the systemic inflammatory milieu after an ischemic insult. Thus, CD40 silencing could emerge as a novel therapeutic strategy in solid organ transplantation.

Multiple active zones in hybrid QM/MM molecular dynamics simulations for large biomolecular systems.

A new QM/MM molecular dynamics approach that can deal with the dynamics of large real systems involving several simultaneous active zones is presented. Multiple, unconnected but interacting quantum regions are treated independently in an ordinary QM/MM approach but in a manner which converges to a unique simulation. The multiple active zones in the hybrid QM/MM molecular dynamics methodology (maz-QM/MM MD) involve molecular dynamics that is driving the whole simulation with several parallel executions of energy gradients within the QM/MM approach that merge into each MD step. The Ewald-summation method is used to incorporate long-range electrostatic interactions among the active zones in conjunction with periodic boundary conditions. To illustrate and ascertain capabilities and limitations, we present several benchmark calculations using this approach. Our results show that the maz-QM/MM MD method is able to provide simultaneous treatment of several active zones of very large proteins such as the Cu-4His-ΔC* cage, a self-assembly of a 24-mer cage-like protein ferritin.

Solvent-induced conformational flexibility of a bicyclic proline analogue: Octahydroindole-2-carboxylic acid.

The conformational preferences of the N-acetyl-N'-methylamide derivatives of the four octahydroindole-2-carboxylic acid (Oic) stereoisomers have been investigated in the gas-phase and in aqueous solution using quantum mechanical calculations. In addition to the conformational effects provoked by the stereochemical diversity of Oic, which presents three chiral centers, results provide evidence of interesting and rather unusual features. The conformational preferences of the Oic stereoisomers in solution are only well described by applying a complete and systematic search process, results achieved by simple re-optimization of the gas-phase minima being very imprecise. This is because the conformational rigidity detected in the gas-phase, which is imposed by the chemical restrictions of the fused bicyclic skeleton, disappears in aqueous solution, the four stereoisomers behaving as flexible molecules in this environment. Thus, in general, the γ-turn is the only minimum energy conformation in the gas-phase while in aqueous solution the helical, polyproline-II and γ-turn motifs are energetically favored. Molecular dynamics simulations indicate that the conformational flexibility predicted by quantum mechanical calculations for the four Oic stereoisomers in solution is satisfactorily reproduced by classical force-fields.

Formation of sparsely tethered bilayer lipid membrane on a biodegradable self-assembled monolayer of poly(lactic acid).

The utilization of biomimetic membranes supported by advanced self-assembled monolayers is gaining attraction as a promising sensing tool. Biomimetic membranes offer exceptional biocompatibility and adsorption capacity upon degradation, transcending their role as mere research instruments to open new avenues in biosensing. This study focused on anchoring a sparsely tethered bilayer lipid membrane onto a self-assembled monolayer composed of a biodegradable polymer, functionalized with poly(ethylene glycol)-cholesterol moieties, for lipid membrane integration. Real-time monitoring via quartz crystal microbalance, coupled with characterization using surface-enhanced infrared absorption spectroscopy and electrochemical impedance spectroscopy, provided comprehensive insights into each manufacturing phase. The resulting lipid layer, along with transmembrane pores formed by gramicidin A, exhibited robust stability. Electrochemical impedance spectroscopy analysis confirmed membrane integrity, successful pore formation, and consistent channel density. Notably, gramicidin A demonstrated sustained functionality as an ion channel upon reconstitution, with its functionality being effectively blocked and inhibited in the presence of calcium ions. These findings mark significant strides in developing intricate biodegradable nanomaterials with promising applications in biomedicine.

Recent Progress in Biomedical Sensors Based on Conducting Polymer Hydrogels.

Biosensors are increasingly taking a more active role in health science. The current needs for the constant monitoring of biomedical signals, as well as the growing spending on public health, make it necessary to search for materials with a combination of properties such as biocompatibility, electroactivity, resorption, and high selectivity to certain bioanalytes. Conducting polymer hydrogels seem to be a very promising materials, since they present many of the necessary properties to be used as biosensors. Furthermore, their properties can be shaped and enhanced by designing conductive polymer hydrogel-based composites with more specific functionalities depending on the end application. This work will review the recent state of the art of different biological hydrogels for biosensor applications, discuss the properties of the different components alone and in combination, and reveal their high potential as candidate materials in the fabrication of all-organic diagnostic, wearable, and implantable sensor devices.

Comment on "A minimal implementation of the AMBER-GAUSSIAN interface for ab initio QM/MM-MD simulation".

We comment upon the recent critique of use of the Program for User Package Interfacing and Linking (PUPIL) system for linking AMBER and GAUSSIAN in a multiscale quantum mechanical/molecular mechanics (QM/MM) simulation (Okamoto et al., J. Comput. Chem. 2011, 32, 932). Specifically, their method for computing forces on the MM particles from the QM region via the GAUSSIAN-03 electrical field was already implemented in PUPIL version 1.3, publicly available beginning December 2009. Some other doubtful characterizations of PUPIL are discussed briefly in the context of current awareness of open-source codes more generally.