High-affinity Interaction Research Articles

Total Synthesis of a PSGL-1 Glycopeptide Analogue for Targeted Inhibition of P-Selectin.

The high affinity interaction between P-selectin glycoprotein ligand-1 (PSGL-1) and P-selectin is mediated by a multimotif glycosulfopeptide (GSP) recognition domain consisting of clustered tyrosine sulfates and a Core 2 O-glycan terminated with sialyl LewisX (C2-O-sLeX). These distinct GSP motifs are much more common than previously appreciated within a wide variety of functionally important domains involved in protein-protein interactions. However, despite the potential of GSPs to serve as tools for fundamental studies and prospects for drug discovery, their utility has been limited by the absence of chemical schemes for synthesis on scale. Herein, we report the total synthesis of GSnP-6, an analogue of the N-terminal domain of PSGL-1, and potent inhibitor of P-selectin. An efficient, scalable, hydrogenolysis-free synthesis of C2-O-sLeX-Thr-COOH was identified by both convergent and orthogonal one-pot assembly, which afforded this crucial building block, ready for direct use in solid phase peptide synthesis (SPPS). C2-O-sLeX-Thr-COOH was synthesized in 10 steps with an overall yield of 23% from the 4-O,5-N oxazolidinone thiosialoside donor. This synthesis represents an 80-fold improvement in reaction yield as compared to prior reports, achieving the first gram scale synthesis of SPPS ready C2-O-sLeX-Thr-COOH and enabling the scalable synthesis of GSnP-6 for preclinical evaluation. Significantly, we established that GSnP-6 displays dose-dependent inhibition of venous thrombosis in vivo and inhibits vaso-occlusive events in a human sickle cell disease equivalent microvasculature-on-a-chip system. The insights gained in formulating this design strategy can be broadly applied to the synthesis of a wide variety of biologically important oligosaccharides and O-glycan bearing glycopeptides.

Discovery of a monoclonal, high-affinity CD8+ T-cell clone following natural hepatitis C virus infection.

CD8+ Tcells recognizing their cognate antigen are typically recruited as a polyclonal population consisting of multiple clonotypes with varying T-cell receptor (TCR) affinity to the target peptide-major histocompatibility complex (pMHC) complex. Advances in single-cell sequencing have increased accessibility toward identifying TCRs with matched antigens. Here we present the discovery of a monoclonal CD8+ T-cell population with specificity for a hepatitis C virus (HCV)-derived human leukocyte antigen (HLA) class I epitope (HLA-B*07:02 GPRLGVRAT) which was isolated directly ex vivo from an individual with an episode of acutely resolved HCV infection. This population was absent before infection and underwent expansion and stable maintenance for at least 2 years after infection as measured by HLA-multimer staining. Furthermore, the monoclonal clonotype was characterized by an unusually long dissociation time (half-life = 794 s and koff = 5.73 × 10-4) for its target antigen when compared with previously published results. A comparison with related populations of HCV-specific populations derived fromthe same individual and a second individual suggested that high-affinity TCR-pMHC interactions may be inherent to epitope identity and shape the phenotype of responses which has implications for rational TCR selection and design in the age of personalized immunotherapies.

Analysis of environmental pollutant Bisphenol F elicited prostate injury targets and underlying mechanisms through network toxicology, molecular docking, and multi-level bioinformatics data integration

Bisphenol F (BPF) has gained prominence as an alternative to bisphenol A (BPA) in various manufacturing applications, yet being detected in diverse environments and posed potential public health risk. This research aims to elucidate the putative toxic targets and underlying molecular mechanisms of prostate injury induced by exposure to BPF through multi-level bioinformatics data, integrating network toxicology and molecular docking. Systematically leveraging multilevel databases, we determined 276 targets related to BPF and prostate injury. Subsequent screenings through STRING and Cytoscape tool highlighted 27 key targets, including BCL2, HSP90AA1, MAPK3, ESR1, and CASP3. GO and KEGG enrichment analyses demonstrated enrichment of targets involved in apoptosis, abnormal hormonal activities, as well as cancer-related signal transduction cascades, ligand-receptor interaction networks, and endocrine system signaling pathways. Molecular docking simulations conducted via Autodock corroborated high-affinity binding interaction between BPF and key targets. The results indicate that BPF exposure can contribute to the initiation and progression of prostate cancer and prostatic hyperplastic by modulating apoptosis and proliferation, altering nerve function in blood vessel endothelial cells, and disrupting androgen metabolism. This study offers theoretical underpinnings for comprehending the molecular mechanisms implicated in BPF-elicited prostatic toxicity, while concomitantly establishing foundational framework for the development of prophylactic and therapeutic strategies for prostatic injuries related to polycarbonate and epoxy resin plastics incorporated with BPF, as well as environments afflicted by elevated levels of these compounds.

Biophysical and NMR analysis reveals binding affinity between HAX1 and CLPB proteins

HCLS1-associated protein X-1 (HAX1) is a multifunctional mitochondrial protein involved in the regulation of apoptosis, a crucial process of programmed cell death, and mRNA processing. Despite its significance, limited structural data is available for HAX1, hindering a comprehensive understanding of its biological function. Notably, the caseinolytic mitochondrial matrix peptidase chaperone subunit B (CLPB) has been identified as an interacting partner of HAX1, yet the biophysical properties and binding affinity governing their interaction remain poorly defined. In this study, we present a thorough biophysical characterization of full-length human HAX1 and CLPB, accomplished through recombinant expression and purification. By employing size exclusion chromatography, dynamic light scattering, and circular dichroism spectroscopy, we successfully established their biophysical properties, revealing contrasting structural features, with CLPB displaying α-helical content and HAX1 exhibiting a disordered nature. Moreover, we employed solution-state nuclear magnetic resonance (NMR) spectroscopy to probe their binding affinity. Our findings demonstrate the formation of stable multimeric complexes between HAX1 and CLPB, and we quantified a dissociation constant in the low range of micro-molar for their high affinity interaction. These results lay the foundation for further in-depth investigations into the dynamics and energetics governing the HAX1-CLPB interaction, ultimately contributing to a comprehensive understanding of their functional mechanisms.

Investigating the Potential Pharmacological Applications of 5-Hydroxy-2 (hydroxymethyl)-4H pyran-4 one through Electronic Characterization and MM-GBSA Studies for Oxidative Stress and Tyrosinase Inhibition: A Quantum Chemical Approach

The study thoroughly examines the possible applications of 5 Hydroxy – 2 (hydroxymethyl) – 4 H pyran – 4 one. Through Quantum chemical analysis, the research rigorously evaluates the compound's properties, including its optoelectronics, geometrical structure, and intermolecular interactions. The geometrical structure parameters were optimized using a 6–311++G(d,p) basis set in the DFT/B3LYP method, and the resulting geometrical factors were then scaled to calculate probable vibrational wavenumbers. The Mulliken charges and MEP map were used to locate electrophilic, nucleophilic regions, and chemical reactivity was described using FMOs and Fukui function assessments. The multiwfn was employed to investigate topological analysis (surface distance projection and Hirshfeld maps). The UV-visible spectrum was used to estimate the absorption of maximum wavelengths, which was then correlated with the TD-DFT, DOS, and band structure investigations. The study also calculated parameters, including Total Energies, ZPE, Entropy, Dipole moment, and Heat Capacity for monomeric and dimeric units. Pharmacokinetics were used to determine the biological characteristics of the compound. The MM-GBSA simulation was performed, and the results suggest that this compound has the potential to be an enhancing anti-oxidant protection agent due to its high binding affinity and intermolecular interactions. These findings are crucial in developing therapeutic agents with pharmacological effects and potential toxicities.

VEGF-R2/CAV-1 Interaction Induced by Resveratrol/Eicosapentaenoic Acid/Docosahexaenoic Acid-Enriched Formulation through Functional Detergent-Resistant Membranes Is Associated with Decreased VEGF-A Release in ARPE-19 Cells.

Omega-3 fatty acids (O3FAs) and resveratrol (RSV) are known to be beneficial for certain eye diseases, such as age-related macular degeneration (AMD). Neovascular AMD is characterized by abnormal blood vessel formation due to the excessive synthesis of vascular endothelial growth factor (VEGF) by retinal pigment epithelium (RPE) cells. The study investigates whether a formulation based on eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), and RSV is capable of counteracting VEGF-A secretion, and elucidates the molecular mechanism. The study finds, using ELISA, that O3FAs/RSV reduces VEGF-A secretion in human RPE cells. This phenomenon is related to the increased interaction between VEGF-receptor 2 (VEGF-R2) and caveolin-1 (CAV-1), a protein of detergent-resistant membranes (DRMs), as determined by co-immunoprecipitation and proximity ligation assay. Using microscale thermophoresis, the study confirms that O3FAs/RSV causes a high-affinity interaction. Isolation and analysis of DRMs reveal that this interaction is concomitant with VEGF-R2 relocalization in DRMs. The depletion of DRMs by a cholesterol-chelating agent blocks the VEGF-R2/CAV-1 interaction and EPA/DHA/RSV-mediated impairment of VEGF production. This specific interaction can provide a new strategy for countering VEGF-A production in human RPE cells and, consequently, reducing neovascularization in AMD. Further preclinical studies involving O3FAs and polyphenols are warranted.

Molecular docking based comparative study of antiviral compounds on SARS-CoV-2 spike protein.

The urgent need for effective therapeutic interventions against SARS-CoV-2 has prompted extensive exploration of potential drug candidates. Among the viral proteins, the spike (S) protein presents an attractive target due to its critical role in viral entry and infection. In this study, we employed molecular docking techniques to investigate the binding affinities and interaction profiles of a panel of active compounds against the SARS-CoV-2 spike protein. Utilising computational simulations, we assessed the binding properties of these compounds within the receptor-binding domain (RBD) and other key regions of the spike protein. Our comparative analysis elucidates the differential binding patterns and identifies promising lead compounds with high binding affinity and favourable interaction profiles. Furthermore, we discuss the implications of these findings for the development of potential therapeutics targeting the SARS-CoV-2 spike protein. Using molecular docking and the Lipinski five rule, this study illustrates possible compounds with strong binding affinities, their molecular interactions, for both naturally occurring and man-made drugs. Computational approach is applied, and it is concluded that, drugs like Withanolide, Dihydroergocristine, Fenebrutinib, and Ergotamine shows binding energies between -8.3 and -9.1 kcal/mol, and are possible candidate for anti covid drug.

Abstract B017: Novel mesothelin-based CAR T cells targeting MUC16 as an intravesical bladder cancer therapy

Abstract Intravesical therapies have been the mainstay of non-muscle invasive bladder cancer (BC) management; however, their efficacy is limited by toxicities, recurrences, and supply shortages. Consequently, many patients are recommended cystectomy, which is fraught with high complication rates. Thus, bladder-sparing treatments present a major, unmet clinical need. Chimeric antigen receptor (CAR) T cell therapy, wherein T cells are engineered to express an artificial receptor to a target, is an immunotherapeutic approach with efficacy in hematologic malignancies. Similar success in solid tumors has been hindered by a lack of suitable targets, reduced T cell infiltration/activity, and major toxicities, including on-target off-tumor effects and cytokine release syndromes. To overcome these limitations, locoregional delivery of CAR T cells is being investigated. Yet, to date, no studies have examined their potential as intravesical therapies. In this study, we used a computational pipeline using large-scale BC transcriptomics data to discover potential CAR targets which met strict criteria of high cell-surface expression on BC and minimal expression on normal tissue. We identified MUC16, a surface-bound mucinous glycoprotein, as a top candidate from this pipeline, which has more reduced pan-tissue expression than targets of precision-guided therapies in BC. Consistent with prior reports, MUC16 transcript and protein levels increase with grade and T stage and correlates with chemotherapeutic resistance. We also find MUC16 expression persists in recurrent tumors after BCG-therapy. To target MUC16, we designed second-generation CARs based on scFv derived from the antibody 3a5 (3a5-28z) and natural-ligands based on the high-affinity MUC16-mesothelin interaction (MSLN-28z) or its truncated binding domain (truncMSLN-28z) which were fused to CD28 co-stimulatory domains and CD3z chains of the T cell receptor. Using human BC lines with a broad range of MUC16 levels, we show MSLN-28z more effectively lyses MUC16+, but not MUC16−, cells than compared to 3a5-28z or truncMSLN-28z CAR T cells. Ablation of MUC16 by CRISPR/Cas9 or modification of MSLN-based CAR to lack signaling domains abolishes the cytotoxicity of MSLN-28z CAR T cells, demonstrating dependency on MUC16 engagement. Using multiplex assays and intracellular cytokine staining, we further demonstrate MSLN-28z CAR T cells have potent polyfunctionality through secretion of cytokines IL-2, IFN-g, and TNF-a by both CD4+ and CD8+ subsets. Last, in immunodeficient mice orthotopically xenografted with HT1376 cells, intravesical delivery of MSLN-28z CAR T cells enhances survival compared to CAR T cells delivered intravenously. This enhanced anti-tumor response correlates with reduced tumor weights and increased T cell infiltration. Notably, intravesically delivered CAR T cells are not detectable in peripheral circulation of tumor-bearing mice. Together, our findings substantiate MUC16 as a targetable antigen in BC and validate MSLN-based CAR T cells as a potential intravesical therapy. Citation Format: Parwiz Abrahimi, Jonathan Khan, Renier Brentjens, Taha Merghoub, Jedd Wolchok. Novel mesothelin-based CAR T cells targeting MUC16 as an intravesical bladder cancer therapy [abstract]. In: Proceedings of the AACR Special Conference on Bladder Cancer: Transforming the Field; 2024 May 17-20; Charlotte, NC. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(10_Suppl):Abstract nr B017.

Implications of Supramolecular Crosslinking on Hydrogel Toughening by Directional Freeze‐Casting and Salting‐Out

AbstractDynamic hydrogel crosslinking captures network reorganization and self‐healing of natural materials, yet is often accompanied by reduced mechanical properties compared to covalent analogs. Toughening is possible in certain materials with processing by directional freeze‐casting and salting‐out, producing hierarchically organized networks with directionally enhanced mechanical properties. The implications of including dynamic supramolecular crosslinking alongside such processes are unclear. Here, a supramolecular hydrogel prepared from homoternary crosslinking by pendant guests with a free macrocycle is subsequently processed by directional freeze‐casting and salting‐out. The resulting hydrogels tolerate multiple cycles of compression. Excitingly, supramolecular affinity dictates the mechanical properties of the bulk hydrogels, with higher affinity interactions producing materials with higher Young's modulus and enhanced toughness under compression. The importance of supramolecular crosslinking is emphasized with a supramolecular complex that is converted in situ into a covalent crosslink. While supramolecular hydrogels do not fracture and spontaneously self‐heal when cut, their covalent analogs fracture under moderate strain and do not self‐heal. This work shows a molecular‐scale origin of bulk hydrogel toughening attributed to affinity and dynamics of supramolecular crosslinking, offering synergy in combination with bulk post‐processing techniques to yield materials with enhanced mechanical properties tunable at the molecular scale for the needs of specific applications.

A Rationally Designed Synthetic Antiviral Peptide Binder Targeting the Receptor-Binding Domain of SARS-CoV-2.

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a novel coronavirus, is the causative agent responsible for the spread of the COVID19 pandemic across the globe. The global impact of the COVID19 pandemic, the successful approval of vaccines for controlling the pandemic, and the further resurgence of COVID19 necessitate the exploration and validation of alternative therapeutic avenues targeting SARS-CoV-2. The initial entry and further invasion by SARS-CoV-2 require strong protein-protein interactions (PPIs) between the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein and the human angiotensin-converting enzyme 2 (ACE2) receptors expressed on the cell surfaces of various tissues. In principle, disruption of the PPIs between the RBD of SARS-CoV-2 and the ACE2 receptor by designer peptides with optimized pharmacology appears to be an ideal choice for potentially preventing viral entry with minimal immunogenicity. In this context, the current study describes a short, synthetic designer peptide (codenamed SR16, ≤18 aa, molecular weight ≤2.5 kDa), which has a few noncoded amino acids, demonstrates a helical conformation in solution, and also engages the RBD of SARS-CoV-2 through a high-affinity interaction, as judged from a battery of biophysical studies. Further, the designer peptide demonstrates resistance to trypsin degradation, appears to be nontoxic to mammalian cells, and also does not induce hemolysis in freshly isolated human erythrocytes. In summary, SR16 appears to be an ideal peptide binder targeting the RBD of SARS-CoV-2, which has the potential for further optimization and development as an antiviral agent targeting SARS-CoV-2.

Evaluation of the Binding Mechanism of Dietary Phytochemical, Ellagic Acid, with Human Transferrin: Spectroscopic, Calorimetric, and Computational Approaches Targeting Neurodegenerative Diseases.

Human transferrin (Htf) is vital in maintaining iron within the brain cells; any disruption results in the development of neurodegenerative diseases (NDs) and other related pathologies, especially Alzheimer's disease (AD). Ellagic acid (EA), a naturally occurring phenolic antioxidant, possesses neuroprotective potential and is present in a broad variety of fruits and vegetables. The current work explores the binding mechanism of dietary polyphenol, EA, with Htf by a combination of experimental and computational approaches. Molecular docking studies unveiled the binding of EA to Htf with good affinity. Molecular dynamic (MD) simulation further provided atomistic details of the binding process, demonstrating a stable Htf-EA complex formation without causing substantial alterations to the protein's conformation. Furthermore, fluorescence binding measurements indicated that EA forms a high-affinity interaction with Htf. Isothermal titration calorimetric measurements advocated the spontaneous nature of binding and also revealed the binding process to be exothermic. In conclusion, the study deciphered the binding mechanism of EA with Htf. The results demonstrated that EA binds with Htf with an excellent affinity spontaneously, thereby laying the groundwork for potential applications of EA in the realm of therapeutics for NDs in the context of iron homeostasis.

Mouse mucosal-associated invariant T cell receptor recognition of MR1 presenting the vitamin B metabolite, 5-(2-oxopropylideneamino)-6-d-ribitylaminouracil

Mucosal-associated invariant T (MAIT) cells can elicit immune responses against riboflavin-based antigens presented by the evolutionary conserved MHC class I related protein, MR1. While we have an understanding of the structural basis of human MAIT cell receptor (TCR) recognition of human MR1 presenting a variety of ligands, how the semi-invariant mouse MAIT TCR binds mouse MR1-ligand remains unknown. Here, we determine the crystal structures of 2mouse TRAV1-TRBV13-2+ MAIT TCR-MR1-5-OP-RU ternary complexes, whose TCRs differ only in the composition of their CDR3β loops. These mouse MAIT TCRs mediate high affinity interactions with mouse MR1-5-OP-RU and cross-recognize human MR1-5-OP-RU. Similarly, a human MAIT TCR could bind mouse MR1-5-OP-RU with high affinity. This cross-species recognition indicates the evolutionary conserved nature of this MAIT TCR-MR1 axis. Comparing crystal structures of the mouse versus human MAIT TCR-MR1-5-OP-RU complexes provides structural insight into the conserved nature of this MAIT TCR-MR1 interaction and conserved specificity for the microbial antigens, whereby key germline-encoded interactions required for MAIT activation are maintained. This is an important consideration for the development of MAIT cell-based therapeutics that will rely on preclinical mouse models of disease.

Furanocoumarins promote proteasomal degradation of viral HBx protein and down-regulate cccDNA transcription and replication of hepatitis B virus

Nucleot(s)ide analogues, the current antiviral treatments against chronic hepatitis B (CHB) infection, are non-curative due to their inability to eliminate covalently closed circular DNA (cccDNA) from the infected hepatocytes. Preclinical studies have shown that coumarin derivatives can effectively reduce the HBV DNA replication. We evaluated the antiviral efficacy of thirty new coumarin derivatives in cell culture models for studying HBV. Furanocoumarins Fc-20 and Fc-31 suppressed the levels of pre-genomic RNA as well as cccDNA, and reduced the secretion of virions, HBsAg and HBeAg. The antiviral efficacies of Fc-20 and Fc31 improved further when used in combination with the hepatitis B antiviral drug Entecavir. There was a marked reduction in the intracellular HBx level in the presence of these furanocoumarins due to proteasomal degradation resulting in the down-regulation of HBx-dependent viral genes. Importantly, both Fc-20 and Fc-31 were non-cytotoxic to cells even at high concentrations. Further, our molecular docking studies confirmed a moderate to high affinity interaction between furanocoumarins and viral HBx via residues Ala3, Arg26 and Lys140. These data suggest that furanocoumarins could be developed as a new therapeutic for CHB infection.

Abstract 5226: A 3D ECM embedded tumoroid platform for testing antibody drugs and engineered TCRs for immune oncology

Abstract We developed a screening platform for immune oncology using an assay based on automated image guided injection of tumoroids in wells of multi-well plates preloaded with a collagen-rich ECM. The identical x-y-z position and size of the ECM-embedded tumoroids in each well facilitates automated real time confocal microscopy and quantitative image analysis algorithms. The model is used to generate quantitative data for T cell recruitment to tumoroids and killing of tumoroids by T cells. We have applied this to screening a panel of CD3:Her2 bispecific antibodies (BsAb) binding with different affinities to CD3 or Her2 or displaying high affinity interactions with different epitopes on Her2. Exposure to fresh, non-activated peripheral blood mononuclear cell (PBMC) derived T cells shows an initial phase of random T cell movement throughout the ECM followed by a BsAb-dependent phase of active T cell recruitment to tumoroids (day 2-4) and a subsequent phase of tumoroid killing (day 4-6). We show that the wave of T cell recruitment following initial T cell-tumoroid contact involves chemotactic signaling. Decreased affinity at the Her2 or CD3 arm can be compensated for by increasing BsAb concentrations. However, we detect major differences in efficacy for different high affinity epitopes. I.e., of two BsAbs interacting with high affinity with distinct Her2 epitopes and each causing effective tumor cell killing in 2D co-culture, only one was able to trigger a wave of T cell recruitment and subsequent tumoroid killing in 3D. We have applied the same setup to testing the efficacy of T cells expressing engineered TCRs aimed at application in adoptive T-cell therapy. Kinetics of experiments using these activated engineered T cells are considerably shorter (24 hours instead of ~6 days) but show a similar pattern of T cell recruitment and subsequent tumoroid killing. We demonstrate successful generation of quantitative data for T cell recruitment and tumoroid killing for engineered T cells targeting tumor antigens expressed on TNBC and uveal melanoma tumoroids. Citation Format: Erik H. J. Danen. A 3D ECM embedded tumoroid platform for testing antibody drugs and engineered TCRs for immune oncology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5226.

Structural and functional characterization of the IgSF21-neurexin2α complex and its related signaling pathways in the regulation of inhibitory synapse organization.

The prevailing model behind synapse development and specificity is that a multitude of adhesion molecules engage in transsynaptic interactions to induce pre- and postsynaptic assembly. How these extracellular interactions translate into intracellular signal transduction for synaptic assembly remains unclear. Here, we focus on a synapse organizing complex formed by immunoglobulin superfamily member 21 (IgSF21) and neurexin2α (Nrxn2α) that regulates GABAergic synapse development in the mouse brain. We reveal that the interaction between presynaptic Nrxn2α and postsynaptic IgSF21 is a high-affinity receptor-ligand interaction and identify a binding interface in the IgSF21-Nrxn2α complex. Despite being expressed in both dendritic and somatic regions, IgSF21 preferentially regulates dendritic GABAergic presynaptic differentiation whereas another canonical Nrxn ligand, neuroligin2 (Nlgn2), primarily regulates perisomatic presynaptic differentiation. To explore mechanisms that could underlie this compartment specificity, we targeted multiple signaling pathways pharmacologically while monitoring the synaptogenic activity of IgSF21 and Nlgn2. Interestingly, both IgSF21 and Nlgn2 require c-jun N-terminal kinase (JNK)-mediated signaling, whereas Nlgn2, but not IgSF21, additionally requires CaMKII and Src kinase activity. JNK inhibition diminished de novo presynaptic differentiation without affecting the maintenance of formed synapses. We further found that Nrxn2α knockout brains exhibit altered synaptic JNK activity in a sex-specific fashion, suggesting functional linkage between Nrxns and JNK. Thus, our study elucidates the structural and functional relationship of IgSF21 with Nrxn2α and distinct signaling pathways for IgSF21-Nrxn2α and Nlgn2-Nrxn synaptic organizing complexes in vitro. We therefore propose a revised hypothesis that Nrxns act as molecular hubs to specify synaptic properties not only through their multiple extracellular ligands but also through distinct intracellular signaling pathways of these ligands.

Membrane Interaction Characteristics of the RTX Toxins and the Cholesterol-Dependence of Their Cytolytic/Cytotoxic Activity.

RTX toxins are important virulence factors produced by a wide range of Gram-negative bacteria. They are secreted as water-soluble proteins that are able to bind to the host cell membrane and insert hydrophobic segments into the lipid bilayer that ultimately contribute to the formation of transmembrane pores. Ion diffusion through these pores leads then to cytotoxic and cytolytic effects on the hosts. Several reports have evidenced that the binding of several RTX toxins to the target cell membrane may take place through a high-affinity interaction with integrins of the β2 family that is highly expressed in immune cells of the myeloid lineage. However, at higher toxin doses, cytotoxicity by most RTX toxins has been observed also on β2-deficient cells in which toxin binding to the cell membrane has been proposed to occur through interaction with glycans of glycosylated lipids or proteins present in the membrane. More recently, cumulative pieces of evidence show that membrane cholesterol is essential for the mechanism of action of several RTX toxins. Here, we summarize the most important aspects of the RTX toxin interaction with the target cell membrane, including the cholesterol dependence, the recent identification in the sequences of several RTX toxins of linear motifs coined as the Cholesterol Recognition/interaction Amino acid Consensus (CRAC), and the reverse or mirror CARC motif, which is involved in the toxin-cholesterol interaction.

Functional regulation of aquaporin dynamics by lipid bilayer composition

With the diversity of lipid-protein interactions, any observed membrane protein dynamics or functions directly depend on the lipid bilayer selection. However, the implications of lipid bilayer choice are seldom considered unless characteristic lipid-protein interactions have been previously reported. Using molecular dynamics simulation, we characterize the effects of membrane embedding on plant aquaporin SoPIP2;1, which has no reported high-affinity lipid interactions. The regulatory impacts of a realistic lipid bilayer, and nine different homogeneous bilayers, on varying SoPIP2;1 dynamics are examined. We demonstrate that SoPIP2;1’s structure, thermodynamics, kinetics, and water transport are altered as a function of each membrane construct’s ensemble properties. Notably, the realistic bilayer provides stabilization of non-functional SoPIP2;1 metastable states. Hydrophobic mismatch and lipid order parameter calculations further explain how lipid ensemble properties manipulate SoPIP2;1 behavior. Our results illustrate the importance of careful bilayer selection when studying membrane proteins. To this end, we advise cautionary measures when performing membrane protein molecular dynamics simulations.

Enhancement of Vitamin C's Protective Effect against Thimerosal-Induced Neurotoxicity in the Cerebral Cortex of Wistar Albino Rats: An In Vivo and Computational Study.

Vitamin C was examined to ameliorate the neurotoxicity of thimerosal (THIM) in an animal model (Wistar albino rats). In our work, oxidative and antioxidative biomarkers such as SOD, LPO, and GSH were investigated at various doses of THIM with or without concurrent vitamin C administration. Furthermore, the adverse effects of THIM on hepatic tissue and cerebral cortex morphology were examined in the absence or presence of associated vitamin C administration. Also, we studied the effect of vitamin C on the metallothionein isoforms (MT-1, MT-2, and MT-3) in silico and in vivo using the RT-PCR assay. The results showed that the antioxidant biomarker was reduced as the THIM dose was raised and vice versa. THIM-associated vitamin C reduced the adverse effects of the THIM dose. The computation studies demonstrated that vitamin C has a lower ΔG of -4.9 kcal/mol compared to -4.1 kcal/mol for THIM to bind to the MT-2 protein, which demonstrated that vitamin C has a greater ability to bind with MT-2 than THIM. This is due to multiple hydrogen bonds that exist between vitamin C and MT-2 residues Lys31, Gln23, Cys24, and Cys29, and the sodium ion represents key stabilizing interactions. Hydrogen bonds involve electrostatic interactions between hydrogen atom donors (e.g., hydroxyl groups) and acceptors (e.g., carbonyl oxygens). The distances between heavy atoms are typically 2.5-3.5 Å. H-bonds provide directed, high-affinity interactions to anchor the ligand to the binding site. The five H-bonds formed by vitamin C allow it to form a stable complex with MT, while THIM can form two H-bonds with Gln23 and Cys24. This provides less stabilization in the binding pocket, contributing to the lower affinity compared to vitamin C. The histopathological morphologies in hepatic tissue displayed an expansion in the portal tract and the hepatocytes surrounding the portal tract, including apoptosis, binucleation, and karyomegaly. The histopathological morphologies in the brain tissue revealed a significant decrease in the number of Purkinje cells due to THIM toxicity. Interestingly, THIM toxicity was associated with hemorrhage and astrogliosis. Both intracellular and vasogenic edema appeared as the concentrations of THIM rose. Finally, vitamin C ameliorated the adverse effect on the cerebral cortex in Wistar albino rats.

Stability-Based Proteomics for Investigation of Structured RNA-Protein Interactions.

RNA-protein interactions are essential to RNA function throughout biology. Identifying the protein interactions associated with a specific RNA, however, is currently hindered by the need for RNA labeling or costly tiling-based approaches. Conventional strategies, which commonly rely on affinity pull-down approaches, are also skewed to the detection of high affinity interactions and frequently miss weaker interactions that may be biologically important. Reported here is the first adaptation of stability-based mass spectrometry methods for the global analysis of RNA-protein interactions. The stability of proteins from rates of oxidation (SPROX) and thermal protein profiling (TPP) methods are used to identify the protein targets of three RNA ligands, the MALAT1 triple helix (TH), a viral stem loop (SL), and an unstructured RNA (PolyU), in LNCaP nuclear lysate. The 315 protein hits with RNA-induced conformational and stability changes detected by TPP and/or SPROX were enriched in previously annotated RNA-binding proteins and included new proteins for hypothesis generation. Also demonstrated are the orthogonality of the SPROX and TPP approaches and the utility of the domain-specific information available with SPROX. This work establishes a novel platform for the global discovery and interrogation of RNA-protein interactions that is generalizable to numerous biological contexts and RNA targets.

Development of Biotinylated Liposomes Encapsulating Metformin for Therapeutic Targeting of Inflammation-Based Diseases.

Inflammation is a physiological response to a damaging stimulus but sometimes can be the cause of the onset of neurodegenerative diseases, atherosclerosis, and cancer. These pathologies are characterized by the overexpression of inflammatory markers like endothelial adhesion molecules, such as Vascular Cell Adhesion Molecule-1 (VCAM-1). In the present work, the development of liposomes for therapeutic targeted delivery to inflamed endothelia is described. The idea is to exploit a three-step pretargeting system based on the biotin-avidin high-affinity interaction: the first step involves a previously described biotin derivative bearing a VCAM-1 binding peptide; in the second step, the avidin derivative NeutrAvidinTM, which strongly binds to the biotin moiety, is injected; the final step is the administration of biotinylated liposomes that would bind to NeutravidinTM immobilized onto VCAM-1 overexpressing endothelium. Stealth biotinylated liposomes, prepared via the thin film hydration method followed by extrusion and purification via size exclusion chromatography, have been thoroughly characterized for their chemico-physical and morphological features and loaded with metformin hydrochloride, a potential anti-inflammatory agent. The three-step system, tested in vitro on different cell lines via confocal microscopy, FACS analysis and metformin uptake, has proved its suitability for therapeutic applications.