Surface Plasmon Resonance Data Research Articles

Predicting Rubisco-Linker Condensation from Titration in the Dilute Phase

The condensation of Rubisco holoenzymes and linker proteins into “pyrenoids,” a crucial supercharger of photosynthesis in algae, is qualitatively understood in terms of “sticker-and-spacer” theory. We derive semianalytical partition sums for small Rubisco-linker aggregates, which enable the calculation of both dilute-phase titration curves and dimerization diagrams. By fitting the titration curves to surface plasmon resonance and single-molecule fluorescence microscopy data, we extract the molecular properties needed to predict dimerization diagrams. We use these to estimate typical concentrations for condensation, and successfully compare these to microscopy observations. Published by the American Physical Society 2024

The Dual-Targeted Fusion Inhibitor Clofazimine Binds to the S2 Segment of the SARS-CoV-2 Spike Protein.

Clofazimine and Arbidol have both been reported to be effective in vitro SARS-CoV-2 fusion inhibitors. Both are promising drugs that have been repurposed for the treatment of COVID-19 and have been used in several previous and ongoing clinical trials. Small-molecule bindings to expressed constructs of the trimeric S2 segment of Spike and the full-length SARS-CoV-2 Spike protein were measured using a Surface Plasmon Resonance (SPR) binding assay. We demonstrate that Clofazimine, Toremifene, Arbidol and its derivatives bind to the S2 segment of the Spike protein. Clofazimine provided the most reliable and highest-quality SPR data for binding with S2 over the conditions explored. A molecular docking approach was used to identify the most favorable binding sites on the S2 segment in the prefusion conformation, highlighting two possible small-molecule binding sites for fusion inhibitors. Results related to molecular docking and modeling of the structure-activity relationship (SAR) of a newly reported series of Clofazimine derivatives support the proposed Clofazimine binding site on the S2 segment. When the proposed Clofazimine binding site is superimposed with other experimentally determined coronavirus structures in structure-sequence alignments, the changes in sequence and structure may rationalize the broad-spectrum antiviral activity of Clofazimine in closely related coronaviruses such as SARS-CoV, MERS, hCoV-229E, and hCoV-OC43.

Abstract 7141: The novel microtubule-destabilizing compound AUS_001 maintains unique binding to the colchicine site of tubulin and elicits reversible cellular effects relative to other anti-tubulin agents

Abstract Our previous work showed that the prenylated hydroxy-stilbene AUS_001 exerts a strong safety profile and potent anti-proliferative responses, as assessed in 30 types of cancer cell lines, stemming from its microtubule destabilization activity. The aim of the current study was to delineate the molecular mechanism of microtubule destabilization by AUS_001 and to provide insight into its high potency and low toxicity. Surface plasmon resonance (SPR) experiments revealed the direct interaction of AUS_001 with tubulin with an apparent equilibrium dissociation constant, Kd, of 2.13 × 10−5M. Size exclusion competition assays and an X-ray crystal structure of the tubulin-AUS_001 complex at 2.1 Å resolution establish ligand binding within the colchicine site on tubulin. Since colchicine-site ligands are well known to inhibit the curved-to-straight conformational transition of tubulin, which is an essential process for microtubule formation, these results readily explain the microtubule-destabilizing activity of the compound. Notably, while both combretastatin A4 (CA-4) and AUS_001 are both colchicine-site stilbene ligands, CA-4 binds in the cis configuration, while AUS_001 maintains a trans configuration leading to a substantially different pocket engagement. Comparison of the tubulin-AUS_001 complex structure with the ones of tubulin-colchicine and tubulin-plinabulin revealed that AUS_001 elicits different rearrangements in the T7 loop of β-tubulin versus colchicine and occupies a different zone of the pocket relative to plinabulin, further elaborating its unique binding properties. Interestingly, AUS_001 exhibits a higher relative affinity than colchicine itself, as assessed by i) an ultrafiltration-based tubulin-ligand release assay and ii) a radioligand colchicine competition assay. However, fitting steady state SPR data for AUS_001 binding to tubulin revealed fast association and dissociation rates and was indicative of reversible binding. The latter finding is corroborated by AUS_001-triggered reverse biological effects including morphological alterations, cell cycle G2/M arrest, and by a decrease of cell viability upon discontinuation of the drug treatment in glioma and pancreatic cancer cells. Conversely, colchicine, CA-4 or paclitaxel administered at the same doses as those applied for AUS_001 failed to reverse the drug-induced phenotypes upon removal resulting in sustained cytotoxicity. In conclusion, we fully characterized the unique binding mode of AUS_001 to the colchicine site of tubulin and elucidated the reversible nature of the target engagement. AUS_001 features a distinctive and reversible molecular interaction with tubulin which provides a plausible explanation for its favorable safety profile compared to other microtubule targeting agents. Citation Format: Herman Lelie, Yao-Chieh Chou, Alastair J. King, Zlata Boiarska, Andrea E. Prota, Michel O. Steinmetz, Marina Koutsioumpa. The novel microtubule-destabilizing compound AUS_001 maintains unique binding to the colchicine site of tubulin and elicits reversible cellular effects relative to other anti-tubulin agents [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 7141.

Computational Deciphering of the Role of S100A8 and S100A9 Proteins and Their Changes in the Structure Assembly Influences Their Interaction with TLR4, RAGE, and CD36.

S100A8 and S100A9 belong to the calcium-binding, damage associated molecular pattern (DAMP) proteins shown to aggravate the pathogenesis of rheumatoid arthritis (RA) through their interaction with the TLR4, RAGE and CD36 receptors. S100A8 and S100A9 proteins tend to exist in monomeric, homo and heterodimeric forms, which have been implicated in the pathogenesis of RA, via interacting with Pattern Recognition receptors (PRRs). The study aims to assess the influence of changes in the structure and biological assembly of S100A8 and S100A9 proteins as well as their interaction with significant receptors in RA through computational methods and surface plasmon resonance (SPR) analysis. Molecular docking analysis revealed that the S100A9 homodimer and S100A8/A9 heterodimer showed higher binding affinity towards the target receptors. Most S100 proteins showed good binding affinity towards TLR4 compared to other receptors. Based on the 50 ns MD simulations, TLR4, RAGE, and CD36 formed stable complexes with the monomeric and dimeric forms of S100A8 and S100A9 proteins. However, SPR analysis showed that the S100A8/A9 heterodimers formed stable complexes and exhibited high binding affinity towards the receptors. SPR data also indicated that TLR4 and its interactions with S100A8/A9 proteins may play a primary role in the pathogenesis of RA, with additional contributions from CD36 and RAGE interactions. Subsequent in vitro and in vivo investigations are warranted to corroborate the involvement of S100A8/A9 and the expression of TLR4, RAGE, and CD36 in the pathophysiology of RA.

The effects of Fe2O3 nanoparticles on catalytic function of human acetylcholinesterase: size and concentration role

Introduction: Fe2O3 NPs can enter cells quickly, pass through the blood-brain barrier and interact with macromolecules. These materials are widely used in different fields, so their risk assessment is among the most critical issues. Acetylcholinesterase (AChE) is a cholinergic enzyme in central and peripheral nervous systems. Methods: In this work, the possible effects of Fe2O3 NPs on the structure and catalytic activity of AChE were investigated using circular dichroism (CD), surface plasmon resonance (SPR), and fluorescence spectroscopies. Results: The outcomes demonstrated that 5 nm Fe2O3 NPs inhibit AChE activity through mixed mechanism. While 50 nm Fe2O3 NPs caused an enhancement in the catalytic activity up to 60 nM. However, higher concentrations of Fe2O3 NPs (above 60 nM) hindered the enzyme activity via mixed mechanism. Fluorescence analysis showed that NPs can quench the fluorescence intensity of AChE that refer to conformational changes. Furthermore, CD results showed that Fe2O3 NPs can reduce the α-helix and β-sheet contents of the enzyme and decrease the stability of AChE. Also, the SPR data analysis showed that the affinity between AChE and Fe2O3 NPs decreased with rising temperature. After treatment with Fe2O3 NPs, the catalytic activity of AChE was assessed in HepG2 cell lines, and the results confirmed the inhibitory effects of Fe2O3 NPs on AChE activity in vivo. Conclusion: These findings provide helpful information about the impact of Fe2O3 NPs on the structure and function of AChE and could offer new insights into the risk assessment of the medical application of nanoparticles.

Homeopathic Formulations of Syzygium jambolanum Alleviate Glycation-Mediated Structural and Functional Modifications of Albumin: Evaluation through Multi-Spectroscopic and Microscopic Approaches.

The growing interest in identifying the mode of action of traditional medicines has strengthened its research. Syzygium jambolanum (Syzyg) is commonly prescribed in homeopathy and is a rich source of phytochemicals. The present study aims to shed light on the anti-glycation molecular mechanism of Syzyg mother tincture (MT), 30c, and 200c on glycated human serum albumin (HSA) by multi-spectroscopic and microscopic approaches. The phytochemicals and antioxidant potential of the Syzyg formulations were estimated by the high-performance liquid chromatography and spectroscopic technique, respectively. Glycation was initiated by incubating HSA with methylglyoxal, three Syzyg formulations, and the known inhibitor aminoguanidine in separate tubes at 37°C for 48 hours. The formation of glycation adducts was assessed by spectrofluorometer and affinity chromatography. The structural modifications were analyzed through circular dichroism, Fourier transform infrared spectroscopy, turbidity, 8-anilinonapthalene-1-sulfonic acid fluorescence, and nuclear magnetic resonance. Further, the formation of the aggregates was examined by thioflavin T, native-polyacrylamide gel electrophoresis, and transmission electron microscopy. Additionally, the functional modifications of glycated HSA were determined by esterase-like activity and antioxidant capacity. The binding analysis of Syzyg formulations with glycated HSA was evaluated by surface plasmon resonance (SPR). Syzyg formulations MT, 30c, and 200c contained gallic acid and ellagic acid as major phytochemicals, with concentrations of 16.02, 0.86, and 0.52 µg/mL, and 227.35, 1.35, and 0.84 µg/mL, respectively. Additionally, all three formulations had remarkable radical scavenging ability and could significantly inhibit glycation compared with aminoguanidine. Further, Syzyg formulations inhibited albumin's structural and functional modifications. SPR data showed that Syzyg formulations bind to glycated HSA with an equilibrium dissociation constant of 1.10 nM. Syzyg formulations inhibited the glycation process while maintaining the structural and functional integrity of HSA.

Levo-tetrahydropalmatine ameliorates neuropathic pain by inhibiting the activation of the Clec7a-MAPK/NF-κB-NLRP3 inflammasome axis

BackgroundBecause of the complex pathogenesis of neuropathic pain (NP), the therapeutic efficacy of existing drugs is not satisfactory. Accumulating studies have indicated that neuroinflammation may play a key role in NP onset and progression. Levo-tetrahydropalmatine (l-THP) has been extensively used for relieving chronic pain for decades. However, its potential mechanisms against NP have not yet been fully elucidated. PurposeExploring and elucidating the therapeutic effect and pharmacological mechanism of l-THP in treating NP. MethodsRNA-seq and bioinformatics analyses were carried out to identify effective target profiling of I-THP in chronic constrictive injury (CCI) rats. The I-THP related hub targets and signaling pathways were obtained via bioinformatics analysis, then subjected to in-depth analyses through experiments in vivo. A gain-of-function study further confirmed the role of Clec7a in l-THP-mediated pain relief. Finally, the interaction between l-THP and Clec7a was verified through molecular docking and surface plasmon resonance (SPR). Resultsl-THP treatment effectively alleviated mechanical and thermal allodynia in NP model rats. Functionally, the I-THP effective targets were mainly enriched in inflammatory response-related pathways. Furthermore, Clec7a-MAPK/NF-κB-NLRP3 inflammasome axis was selected as one of the potential pathways of l-THP against NP. Mechanically, l-THP markedly reduced CCI-induced Clec7a overexpression, significantly inhibited the Clec7a-triggered phosphorylation of MAPK and NF-κB-p65, and decreased the expression of pyroptosis-related protein NLRP3 and Caspase-1-p20. The analgesic effect of l-THP on NP was partly eliminated when transfecting the overexpression vector virus pLVSO5Clec7a. Importantly, molecular docking and SPR data revealed that l-THP directly binds with the Clec7a protein. ConclusionThis study is the first to indicate that l-THP may exert an analgesic effect through inhibiting neuroinflammation via the Clec7a-MAPK/NF-κB-NLRP3 inflammasome axis, supporting the clinical utility of l-THP in NP therapy.

Production and characterization of monoclonal antibodies for the detection of the hepatitis C core antigen.

Background: Despite highly effective treatments to cure hepatitis C, almost 80% of chronically HCV-infected people are not treated, as they are unaware of their infection. Diagnostic rates and linkage to care must be substantially improved to reverse this situation. The HCV core antigen (HCVcAg) is a highly conserved protein that can be detected in the blood of HCV-infected patients and indicates active infection. Aim: To produce murine monoclonal antibodies against HCVcAg suitable for rapid and inexpensive tests to detect HCV infection. Methods: BALB/c mice were sequentially inoculated with purified recombinant HCVcAg from Gt1a, Gt3a, Gt4a, and Gt1b genotypes. Hybridomas producing the desired monoclonal antibodies were selected, and the reactivity of antibodies against HCVcAg from various genotypes was tested by Western blotting and dot blotting. The binding kinetics of the antibodies to purified HCVcAg was analyzed by surface plasmon resonance (SPR), and their ability to detect HCVcAg was tested by double antibody sandwich ELISA (DAS-ELISA). Results: Four specific monoclonal antibodies (1C, 2C, 4C, and 8C) were obtained. 1C, 2C, and 4C recognized HCVcAg of all genotypes tested (Gt1a, Gt1b, Gt2a, Gt3a, and Gt4a), while 8C did not recognize the Gt2a and Gt3a genotypes. Based on SPR data, the antibody-HCVcAg complexes formed are stable, with 2C having the strongest binding properties. DAS-ELISA with different antibody combinations easily detected HCVcAg in culture supernatants from HCV-infected cells. Conclusion: Specific and cross-reactive anti-HCVcAg monoclonal antibodies with strong binding properties were obtained that may be useful for detecting HCVcAg in HCV-infected samples.

TitrationAnalysis: a tool for high throughput binding kinetics data analysis for multiple label-free platforms.

Label-free techniques including Surface Plasmon Resonance (SPR) and Biolayer Interferometry (BLI) are biophysical tools widely used to collect binding kinetics data of bimolecular interactions. To efficiently analyze SPR and BLI binding kinetics data, we have built a new high throughput analysis tool named the TitrationAnalysis. It can be used as a package in the Mathematica scripting environment and ultilize the non-linear curve-fitting module of Mathematica for its core function. This tool can fit the binding time course data and estimate association and dissociation rate constants ( k a and k d respectively) for determining apparent dissociation constant ( K D) values. The high throughput fitting process is automatic, requires minimal knowledge on Mathematica scripting and can be applied to data from multiple label-free platforms. We demonstrate that the TitrationAnalysis is optimal to analyze antibody-antigen binding data acquired on Biacore T200 (SPR), Carterra LSA (SPR imaging) and ForteBio Octet Red384 (BLI) platforms. The k a, k d and K D values derived using TitrationAnalysis very closely matched the results from the commercial analysis software provided specifically for these instruments. Additionally, the TitrationAnalysis tool generates user-directed customizable results output that can be readily used in downstream Data Quality Control associated with Good Clinical Laboratory Practice operations. With the versatility in source of data input source and options of analysis result output, the TitrationAnalysis high throughput analysis tool offers investigators a powerful alternative in biomolecular interaction characterization.

β-Glucan and Fatty Acid Based Mucoadhesive Carrier for Gastrointestinal Tract Specific Local and Sustained Drug Delivery.

The oral route is considered the most convenient route of drug administration for both systemic and local delivery. Besides stability and transportation, another unmet but important issue regarding oral medication is retention duration within the specific region of the gastrointestinal (GI) tract. We hypothesize that an oral vehicle that can adhere and maintain retention within the stomach for a longer duration can be more effective to treat stomach-related diseases. Therefore, in this project, we developed a carrier that is highly specific to the stomach and maintains its retention for a longer duration. We developed a vehicle composed of β-Glucan And Docosahexaenoic Acid (GADA) to observe its affinity and specificity to the stomach. GADA forms a spherical-shaped particle with negative zeta potential values that vary based on the feed ratio of docosahexaenoic acid. Docosahexaenoic acid is an omega-3 fatty acid that has transporters and receptors throughout the GI tract, such as CD36, plasma membrane-associated fatty acid-binding protein (FABP (pm)), and a family of fatty acid transport proteins (FATP1-6). The in vitro studies and characterization data showed that GADA has the capability to carry a payload of hydrophobic molecules and specifically deliver the payload to the GI tract, exert its therapeutic effects, and help to maintain stability for more than 12 h in the gastric and intestinal fluid. The particle size and surface plasmon resonance (SPR) data showed that GADA has a strong binding affinity with mucin in the presence of simulated gastric fluids. We observed a comparatively higher drug release of lidocaine in gastric juice than that in intestinal fluids, demonstrating the influence of the pH values of the media on drug-release kinetics. In vivo and ex vivo imaging of mice demonstrated that GADA maintains its retention within the stomach for at least 4 hr. This stomach-specific oral vehicle holds strong promise to translate various injectable therapeutic drugs to oral form upon further optimizations.

Binding Behavior between Transforming-Growth-Factor-Beta1 and Its Receptor Reconstituted in Biomimetic Membranes

Transforming growth factor β1 (TGF-β1) is critical to cell differentiation, proliferation, and apoptosis. It is important to understand the binding affinity between TGF-β1 and its receptors. In this study, their binding force was measured using an atomic force microscope. Significant adhesion was induced by the interaction between the TGF-β1 immobilized on the tip and its receptor reconstituted in the bilayer. Rupture and adhesive failure occurred at a specific force around 0.4~0.5 nN. The relationship of the force to loading rate was used to estimate the displacement where the rupture occurred. The binding was also monitored in real time with surface plasmon resonance (SPR) and interpreted with kinetics to acquire the rate constant. Using the Langmuir adsorption, the SPR data were analyzed to estimate equilibrium and association constants to be approximately 107 M-1 and 106 M-1 s-1. These results indicated that the natural release of the binding seldom occurred. Furthermore, the degree of binding dissociation, confirmed by the rupture interpretation, supported that the reverse of the binding hardly happened.

Abstract 1387: Novel thienopyrimidine-hydrazinyl analog, TPH104m inhibits mitochondrial respiration and induces caspase-independent cell death in triple-negative breast cancer cells

Abstract A triple negative breast cancer (TNBC) is an aggressive and difficult-to-treat breast cancer subtype. Neoadjuvant chemotherapy using apoptosis-inducing taxanes and/or anthracyclines has been shown to produce early therapeutic responses. Unfortunately, drug resistance often results from mutations in apoptotic pathways, which can lead to metastasis and poor prognosis. There are emerging studies suggesting that TNBC tumors display altered mitochondrial dynamics and have overexpressed dynamin related protein 1 (Drp1), which drives mitochondrial fission. Drp1 deregulation also influences metabolic changes and mitochondrial energetics, which support TNBC tumor growth. Therefore, bypassing apoptosis signaling cascade, suppressing Drp1 and reversing aberrant mitochondrial dynamics may be an effective therapy for TNBC. We report here for the first time the identification of novel thienopyrimidine-hydrazinyl analog of parent TPH104, namely, TPH104m, which inhibits Drp1 phosphorylation and induces a non-apoptotic TNBC cell death. TPH104m significantly inhibited TNBC proliferation at nanomolar concentrations, and was more selective for TNBC than normal human mammary epithelial cells. TPH104m induced a unique type of non-apoptotic cell death, where cells swelled without shrinkage, nuclear fragmentation or apoptotic bleb formation typical of apoptosis. Moreover, TPH104m did not induce the cleavage of initator (caspase-8, -9) and executioner caspases (caspase-3, -7), and zVAD.fmk, a pan-caspase inhibitor, did not rescue TNBC cell death when incubated with TPH104m. Furthermore, TPH104m did not significantly increase reactive oxygen species (ROS) production in BT-20 cells compared to Paclitaxel treated cells. Although mitochondrial membrane potential (MMP) was significantly reduced, cytochrome C release was not increased, but instead decreased, explaining why MMP loss did not lead to apoptosis. TPH104m remarkably downregulated the phosphorylated and total forms of Drp1 protein in TNBC cells. A docking-based reverse screening approach and Surface Plasmon Resonance (SPR) data indicated that TPH104m binds to Drp1 more strongly than Mdivi-1, a weak non-specific Drp1 inhibitor. A complete and partial Drp1 KO cell line was created in SUM-159 TNBC cells to investigate the role of Drp1 in TPH104m-induced non-apoptotic cell death. Genetically deleting Drp1 from TNBC cells reduced TPH104m's cytotoxic potential suggesting Drp1's role in TPH104m's anticancer mechanism. Moreover, mito-stress assay showed that TPH104m severely impaired oxygen consumption rate, resulting in decreased ATP production and inhibition of mitochondrial respiration. Development of alternative treatments for TNBC will be facilitated by a deeper understanding of mitochondrial role in non-apoptotic cell death. Citation Format: Saloni Malla, David Terrero, Sushma Karki, Mariam Sami Abou-Dahech, Shikha Kumari, Amit K. Tiwari. Novel thienopyrimidine-hydrazinyl analog, TPH104m inhibits mitochondrial respiration and induces caspase-independent cell death in triple-negative breast cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1387.

Controlling the Binding Efficiency of Surface Confined Antibodies through the Design of Mixed Self‐Assembled Monolayers

AbstractA plethora of different electronic and optoelectronic devices have been developed lately, for biosensing applications (e.g., label‐free, fast, and easier to operate) based on a detecting interface accommodating the biorecognition elements, anchored by thiolate self‐assembled monolayers (SAMs) on a gold surface. Here, a surface plasmon resonance (SPR) characterization of anti‐p24 anchored on different SAMs is performed to investigate the effect of the SAM structure on the antibodies’ packing efficiency and the sensors’ analytical figures of merit. Notably, the mixed SAM deposited from a solution 10:1 of 3‐mercaptopropionic acid and 11‐mercaptoundecanoic acid (11MUA) is compared to that resulting from a solution 10:1 of ad hoc synthesized N‐(2‐hydroxyethyl)‐3‐mercaptopropanamide (NMPA)/11MUA. Despite the improvement in the anti‐p24 surface coverage registered using the 11MUA/NMPA SAM, the latter produces a significant decrease in the antibodies’ binding efficiency against human immunodeficiency virus p24 protein. To provide a molecular rationale behind the SPR data, density functional theory calculations are also undertaken. A comprehensive physical view of the main competing phenomena affecting the biorecognition events at a biofunctionalized gold detecting interface is represented here.

A fully human connective tissue growth factor blocking monoclonal antibody ameliorates experimental rheumatoid arthritis through inhibiting angiogenesis

BackgroundConnective tissue growth factor (CTGF) plays a pivotal role in the pathogenesis of rheumatoid arthritis (RA) by facilitating angiogenesis and is a promising therapeutic target for RA treatment. Herein, we generated a fully human CTGF blocking monoclonal antibody (mAb) through phage display technology.ResultsA single-chain fragment variable (scFv) with a high affinity to human CTGF was isolated through screening a fully human phage display library. We carried out affinity maturation to elevate its affinity for CTGF and reconstructed it into a full-length IgG1 format for further optimization. Surface plasmon resonance (SPR) data showed that full-length antibody IgG mut-B2 bound to CTGF with a dissociation constant (KD) as low as 0.782 nM. In the collagen-induced arthritis (CIA) mice, IgG mut-B2 alleviated arthritis and decreased the level of pro-inflammatory cytokines in a dose-dependent manner. Furthermore, we confirmed that the TSP-1 domain of CTGF is essential for the interaction. Additionally, the results of Transwell assays, tube formation experiments, and chorioallantoic membrane (CAM) assays showed that IgG mut-B2 could effectively inhibit angiogenesis.ConclusionThe fully human mAb that antagonizes CTGF could effectively alleviate arthritis in CIA mice, and its mechanism is tightly associated with the TSP-1 domain of CTGF.

Interaction of bioactive kaempferol with HMGB1: Investigation by multi-spectroscopic and molecular simulation methods

Chronic and persistent inflammation associated with excessive high mobility group protein 1 (HMGB1) is a risk factor for various diseases. Dietary intake of kaempferol has been proven to be effective in reducing HMGB1 levels and the degree of inflammation, but the structural mechanism remains unclear. In this context, we first investigated the interaction between bioactive kaempferol and HMGB1 using multi-spectroscopic and molecular simulation techniques. The surface plasmon resonance (SPR) data indicated that kaempferol binds directly to HMGB1 with a Kd value of 2.89 × 10−5 M. Binding of kaempferol with HMGB1 led to the intrinsic fluorescence quenching and modest secondary structure change of HMGB1 supported by fluorescence spectrometry and circular dichroism (CD). Using dynamic light scattering (DLS), it was found that kaempferol induced the aggregation of HMGB1 protein complex to form larger particles. On HMGB1-activated RAW264.7 cells, kaempferol co-incubation exhibited a remarkable inhibitory effect on nitric oxide (NO) release with an IC50 value of 5.02 μM, which was lower than that of quercetin. In silico, kaempferol binds to HMGB1 mainly through hydrogen bonds and hydrophobic forces. Collectively, our study showed kaempferol as a potential HMGB1 inhibitor, mainly acting by direct binding to HMGB1 and inducing its conformational changes, which provides clues for the treatment of chronic inflammation by kaempferol.

Monomeric and dimeric states of human ZO1-PDZ2 are functional partners of the SARS-CoV-2 E protein

The Envelope (E) protein of SARS-CoV-2 plays a key role in virus maturation, assembly, and virulence mechanisms. The E protein is characterized by the presence of a PDZ-binding motif (PBM) at its C-terminus that allows it to interact with several PDZ-containing proteins in the intracellular environment. One of the main binding partners of the SARS-CoV-2 E protein is the PDZ2 domain of ZO1, a protein with a crucial role in the formation of epithelial and endothelial tight junctions (TJs). In this work, through a combination of analytical ultracentrifugation analysis and equilibrium and kinetic folding experiments, we show that ZO1-PDZ2 domain is able to fold in a monomeric state, an alternative form to the dimeric conformation that is reported to be functional in the cell for TJs assembly. Importantly, surface plasmon resonance (SPR) data indicate that the PDZ2 monomer is fully functional and capable of binding the C-terminal portion of the E protein of SARS-CoV-2, with a measured affinity in the micromolar range. Moreover, we present a detailed computational analysis of the complex between the C-terminal portion of E protein with ZO1-PDZ2, both in its monomeric conformation (computed as a high confidence AlphaFold2 model) and dimeric conformation (obtained from the Protein Data Bank), by using both polarizable and nonpolarizable simulations. Together, our results indicate both the monomeric and dimeric states of PDZ2 to be functional partners of the E protein, with similar binding mechanisms, and provide mechanistic and structural information about a fundamental interaction required for the replication of SARS-CoV-2.

Intercalation of anticancer drug mitoxantrone into DNA: Studied by spectral and surface plasmon resonance methods

Studying DNA interaction with different drugs is interesting and important in discovering the interaction mechanism and developing novel drugs. Mitoxantrone (MTX) is a potent antitumor drug used to treat certain types of cancer. In this work, we evaluated the binding strength of MTX to 16 base pair double strands (ds) DNA. For the first time, this work investigates the intercalation of anticancer drugs into DNA by spectral fluorescence spectroscopy and SPR (surface plasmon resonance) based methods. Furthermore, the thermodynamic and kinetic parameters, including KD, KA, entropy change (ΔS), enthalpy change (ΔH), and ΔG, were calculated using different concentrations of ds DNA at three different temperatures. The results indicated that MTX binding to DNA was an exothermic and spontaneous process. The negative value of both ΔH and ΔS calculated by SPR and fluorescence data analysis showed that hydrogen bonding was the major binding force for the complexation of MTX to DNA. In addition, fluorescence data analysis revealed that MTX could quench the DNA fluorescence via the static quenching mechanism. This study shows that the investigation of intercalation anticancer drugs into DNA can be studied by spectral methods and can be investigated using SPR based method, and obtained data from the SPR method is as reliable as the fluorescence method. The present work shows hydrogen bonding is the major binding force in intercalating MTX to DNA.

Metal-chelating activity of soy and pea protein hydrolysates obtained after different enzymatic treatments from protein isolates

Soy and pea proteins are two rich sources of essential amino acids. The hydrolysis of these proteins reveals functional and bioactive properties of the produced small peptide mixtures. In our study, we employed the hydrolysis of soy and pea protein isolates with the endopeptidases Alcalase® and Protamex®, used alone or followed by the exopeptidase Flavourzyme®. The sequential enzyme treatments were the most efficient regarding the degree of hydrolysis. Then, soy and pea protein hydrolysates (SPHs and PPHs, respectively) were ultrafiltrated in order to select peptides of molecular weight ≤ 1 kDa. Whatever the protein source or the hydrolysis treatment, the hydrolysates showed similar molecular weight distributions and amino acid compositions. In addition, all the ultrafiltrated hydrolysates possess metal-chelating activities, as determined by UV-spectrophotometry and Surface Plasmon Resonance (SPR). However, the SPR data revealed better chelating affinities in SPHs and PPHs when produced by sequential enzymatic treatment.

Probing the Interactions of Lamotrigine and Phenobarbital with Tau Protein: Experimental and Molecular Modeling Studies.

Tau, as a small protein in neurons, plays a main role in stabilizing and assembling the internal microtubules. Here, the effects of antiepileptic drugs, including lamotrigine (LTG) and phenobarbital (PHB), on tau protein structure have been investigated by surface plasmon resonance (SPR), fluorescence spectroscopy along molecular modeling. Fluorescence data analysis revealed that both drugs quench the intrinsic emission intensity of tau protein via a static quenching mechanism. Analysis of SPR data at three different temperatures revealed that binding of LTG and PHB to tau protein leads to a decrease and increase in equilibrium constants (KD) values with increasing temperature, respectively. Therefore, the affinity of LTG decreases and PHB increases with increasing temperature. In addition, molecular docking studies indicated that both LTG and PHB bind to the S1 pocket of tau protein. Our data demonstrated the preventive effect of two important antiepileptic pharmaceuticals on the aggregation of tau protein. Given that any damage to the tau protein possibly leads to neurodegenerative diseases, this study can provide useful and important information and a basis for further research and study to treat tauopathy.

Chebulinic and chebulagic acid binding with serum proteins: biophysical and molecular docking approach

Chebulinic acid (CHN) and chebulagic acid (CHG) have been known for centuries for their anti-cancer, anti-diabetes, HIV and anti-inflammatory properties. In this study, the interaction of these phytochemicals CHN/CHG, with the two major transport proteins for various drugs, human serum albumin (HSA) and α-1-acid glycoprotein (AGP), was unraveled by using several spectroscopic techniques and computational methods. The binding of CHN/CHG quenches the HSA/AGP fluorescence intensities, and also these phytochemicals are bound strongly to HSA/AGP proteins. An apparent decrease in fluorescence intensities of CHN/CHG-HSA and CHN/CHG-AGP complex showed the static mode of fluorescence quenching. Furthermore, the intrinsic fluorescence and using site-specific markers ibuprofen competing with these molecules, thereby replacing it in the binding site of subdomain IIIA. The computational methods substantiated the experimental findings, revealing that CHN interacted with Lys414A, Glu492A, Glu492A and Lys413A residues of subdomain IIIA of HSA and for CHG showed the interaction with Lys545A and Lys413A residues of subdomain IIIA of HSA. Fluorescence and surface plasmon resonance data unveiled a previously unreported binding event between CHN/CHG and HSA; the determined binding affinities of both compounds were slightly higher for HSA than AGP. A change in functionality of protein confirmed the esterase‐like activity of HSA in the presence of CHG/CHN upon binding with CHG/CHN. Displacement and circular dichroism (CD) experiments analysis showed that the two CHN/CHG and binding specifically to IIIA subdomain on HSA results in the conformational changes in the HSA. Thus, CD revealed a few conformational changes in HSA due to CHN/CHG. The binding of these two phytochemicals to the plasma proteins would give a path to develop new inspired drug molecules for chronic diseases. Communicated by Ramaswamy H. Sarma