Monitoring drug–serum protein interactions for early ADME prediction through Surface Plasmon Resonance technology

Nature-Inspired 1-Phenylpyrrolo[2,1-a]isoquinoline Scaffold for Novel Antiproliferative Agents Circumventing P-Glycoprotein-Dependent Multidrug Resistance

Previous studies have shown that some lamellarin-resembling annelated azaheterocyclic carbaldehydes and related imino adducts, sharing the 1-phenyl-5,6-dihydropyrrolo[2,1-a]isoquinoline (1-Ph-DHPIQ) scaffold, are cytotoxic in some tumor cells and may reverse multidrug resistance (MDR) mediated by P-glycoprotein (P-gp). Herein, several novel substituted 1-Ph-DHPIQ derivatives were synthesized which carry carboxylate groups (COOH, COOEt), nitrile (CN) and Mannich bases (namely, morpholinomethyl derivatives) in the C2 position, as replacements of the already reported aldehyde group. They were evaluated for antiproliferative activity in four tumor cell lines (RD, HCT116, HeLa, A549) and for the ability of selectively inhibiting P-gp-mediated MDR. Lipophilicity descriptors and molecular docking calculations helped us in rationalizing the structure-activity relationships in the P-gp inhibition potency of the investigated 1-Ph-DHPIQs. As a main outcome, a morpholinomethyl Mannich base (8c) was disclosed which proved to be cytotoxic to all the tested tumor cell lines in the low micromolar range (IC50 < 20 μM) and to inhibit in vitro the efflux pumps P-gp and MRP1 responsible for MDR, with IC50s of 0.45 and 12.1 μM, respectively.

Anti-Aggregative and Protective Effects of Vicenin-2 on Heat and Oxidative Stress-Induced Damage on Protein Structures

Vicenin-2, a flavonoid categorized as a flavones subclass, exhibits a distinctive and uncommon C-glycosidic linkage. Emerging evidence challenges the notion that deglycosylation is not a prerequisite for the absorption of C-glycosyl flavonoid in the small intestine. Capitalizing on this experimental insight and considering its biological attributes, we conducted different assays to test the anti-aggregative and antioxidant capabilities of vicenin-2 on human serum albumin under stressful conditions. Within the concentration range of 0.1-25.0 μM, vicenin-2 effectively thwarted the heat-induced HSA fibrillation and aggregation of HSA. Furthermore, in this study, we have observed that vicenin-2 demonstrated protective effects against superoxide anion and hydroxyl radicals, but it did not provide defense against active chlorine. To elucidate the underlying mechanisms, behind this biological activity, various spectroscopy techniques were employed. UV-visible spectroscopy revealed an interaction between HSA and vicenin-2. This interaction involves the cinnamoyl system found in vicenin-2, with a peak of absorbance observed at around 338 nm. Further evidence of the interaction comes from circular dichroism spectrum, which shows that the formation of bimolecular complex causes a reduction in α-helix structures. Fluorescence and displacement investigations indicated modifications near Trp214, identifying Sudlow's site I, similarly to the primary binding site. Molecular modeling revealed that vicenin-2, in nonplanar conformation, generated hydrophobic interactions, Pi-pi stacking, and hydrogen bonds inside Sudlow's site I. These findings expand our understanding of how flavonoids bind to HSA, demonstrating the potential of the complex to counteract fibrillation and oxidative stress.

Highly sensitive label-free biosensor: graphene/CaF2 multilayer for gas, cancer, virus, and diabetes detection with enhanced quality factor and figure of merit

One of the primary goals for the researchers is to create a high-quality sensor with a simple structure because of the urgent requirement to identify biomolecules at low concentrations to diagnose diseases and detect hazardous chemicals for health early on. Recently graphene has attracted much interest in the field of improved biosensors. Meanwhile, graphene with new materials such as CaF2 has been widely used to improve the applications of graphene-based sensors. Using the fantastic features of the graphene/CaF2 multilayer, this article proposes an improvement sensor in the sensitivity (S), the figure of merit (FOM), and the quality factor (Q). The proposed sensor is based on the five-layers graphene/dielectric grating integrated with a Fabry-Perot cavity. By tuning graphene chemical potential (µc), due to the semi-metal features of graphene, the surface plasmon resonance (SPR) waves excited at the graphene/dielectric boundaries. Due to the vertical polarization of the source to the gratings and the symmetry of the electric field, both corners of the grating act as electric dipoles, and this causes the propagation of plasmonic waves on the graphene surface to propagate towards each other. Finally, it causes Fabry-Perot (FP) interference on the surface of graphene in the proposed structure's active medium (the area where the sample is located). In this article, using the inherent nature of FP interference and its S to the environment's refractive index (RI), by changing a minimal amount in the RI of the sample, the resonance wavelength (interferometer order) shifts sharply. The proposed design can detect and sense some cancers, such as Adrenal Gland Cancer, Blood Cancer, Breast Cancer I, Breast Cancer II, Cervical Cancer, and skin cancer precisely. By optimizing the structure, we can achieve an S as high as 9000 nm/RIU and a FOM of about 52.14 for the first resonance order (M1). Likewise, the remarkable S of 38,000 nm/RIU and the FOM of 81 have been obtained for the second mode (M2). In addition, the proposed label-free SPR sensor can detect changes in the concentration of various materials, including gases and biomolecules, hemoglobin, breast cancer, diabetes, leukemia, and most alloys, with an accuracy of 0.001. The proposed sensor can sense urine concentration with a maximum S of 8500 nm/RIU and cancers with high S in the 6000 nm/RIU range to 7000 nm/RIU. Also, four viruses, such as M13 bacteriophage, HIV type one, Herpes simplex type 1, and influenza, have been investigated, showing Maximum S (for second resonance mode of λR(M2) of 8000 nm/RIU (λR(M2) = 11.2 µm), 12,000 nm/RIU (λR(M2) = 10.73 µm), 38,000 nm/RIU (λR(M2) = 11.78 µm), and 12,000 nm/RIU (λR(M2) = 10.6 µm), respectively, and the obtained S for first resonance mode (λR(M1)) for mentioned viruses are 4740 nm/RIU (λR(M1) = 8.7 µm), 8010 nm/RIU (λR(M1) = 8.44 µm), 8100 nm/RIU (λR(M1) = 10.15 µm), and 9000 (λR(M1) = 8.36 µm), respectively.

New Methodology for Determining Plasma Protein Binding Kinetics Using an Enzyme Reporter Assay Coupling with High-Resolution Mass Spectrometry

Determination of drug binding kinetics in plasma is important yet extremely challenging. Accordingly, we introduce "dynamic free fraction" as a new binding parameter describing drug-protein binding kinetics. We demonstrate theoretically and experimentally that the dynamic free fraction can be determined by coupling the drug binding assay with a reporter enzyme in combination with high-resolution mass spectrometry measuring the relative initial steady-state rates of enzymatic reactions in the absence and presence of matrix proteins. This novel and simple methodology circumvents a long-standing challenge inherent in existing methods for determining binding kinetics constants, such as k_on and k_off, and enables assessment of the impact of protein binding kinetics on pharmaceutical properties of drugs. As demonstrated with nine model drugs, the predicted liver extraction ratio, a measure of efficiency of drug removal by the liver, correlates significantly better to the observed extraction ratio when using the dynamic free fraction (f_D) in place of the unbound fraction (f_u) of the drug in plasma. Similarly, the in vivo hepatic clearance of these drugs, a measure of liver drug elimination, is highly comparable to the clearance values calculated with the dynamic free fraction (f_D), which is markedly better than those calculated with the unbound fraction (f_u). In contrast to the prevailing view, these results indicate that protein binding kinetics is an important pharmacokinetic property of a drug. As plasma protein binding is one of the most important drug properties, this new methodology may represent a breakthrough and could have a real impact on the field.

Alterations in the conformation and function of human serum albumin induced by the binding of methyl hydrogen phthalate

Phthalate esters (PAEs) are widely used as plasticizer components in production. Methyl hydrogen phthalate (MHP) is a metabolite of dimethyl phthalate (DMP, a kind of PAEs), and its toxic residues accumulate in the nature and can enter the human body. Here, the interaction between MHP and human serum albumin (HSA) was probed by using multi-spectral, computer simulations, and biochemical techniques. The results showed that MHP was spontaneously embedded in site I of HSA to form a complex by H-bonds and van der Waals forces (ΔH < 0, ΔS < 0). The binding constant (K_a) of the HSA-MHP system was 1.136 ± 0.026 × 10⁴ M^-1 (298 K). The combination of MHP produced conformational variations of HSA, as shown by the 3D fluorescence spectrum, CD spectra, and molecular dynamics simulation. Additionally, molecular docking indicated that MHP was surrounded by multiple residues, such as Lys199, Leu203, Phe206, and Trp214. Specifically, Lys199 and Trp214 exerted a crucial effect on the interaction of HSA and MHP. The residues with important energy contribution were mostly located in site I. The ASA values of the aromatic amino acids of HSA changed after combining with MHP. The R_g and SASA values of HSA increased after adding MHP, suggesting that the structure of HSA was less compact. Moreover, the esterase-like activity of HSA increased after adding MHP to HSA, indicating that MHP may disturb the normal physiological activities in the human body. This study was helpful to understand the biological function of MHP and provided some insights for its side effect in the human body.

Study on the action mechanism of the peptide compounds of Wuguchong on diabetic ulcers, based on UHPLC-Q-TOF-MS, network pharmacology and experimental validation

ETHNOPHARMACOLOGICAL RELEVANCE

Diabetic foot ulcers mainly refer to people who are initially diabetic and do not have peripheral neuropathy or peripheral vascular disease, but have developed foot infection, septicemia, and ulceration. Diabetic trauma disease is characterized by high sugar and very slow wound healing, which is the reason why some patients with severe diabetic trauma require amputation. Prolonged hyperglycemia can lead to changes in bodily functions and endocrine changes, which can lead to permeability damage of epidermal tissue structure, microvascular damage and, in more severe cases, nerve damage, which are also the main causes of diabetic trauma. Small molecule peptides have various biological activities, such as: lowering blood pressure, antibacterial and wound healing activities, etc. It is a drug recorded in classical Chinese medicine, it is safer to use natural active peptides to treat wounds compared to the listed drugs, and there are no side effects in its use.The wound healing effect of Wuguchong dry product has been confirmed but the mechanism is still unclear, whether it is related to the small molecule active peptides contained in it remains to be studied.

AIM OF STUDY

Objective To investigate the potential mechanism of the peptide compounds of Wuguchong (PCW) on diabetic wound healing and the relevant targets in the pathway associated with the treatment of diabetic ulcers using a systematic pharmacological and pharmacological experimental validation approach.

METHODS

1) PCW was prepared by enzymatic digestion of TCMW and analyzed by UHPLC-Q-TOF-MS. 2) Further screening of the active chemical components of PCW using PubChem, Swiss Target Prediction data. 3) Prediction of its targets using Drug Bank, CTD, and Genecards databases. 4) Construct protein/gene interactions network diagrams for PCWs acting by using Cytoscape 3.7.0 software. 5) GO and KEGG analysis of PCW targets were performed by David database. 6) Validated by AO/EB staining, scratching and in vitro tube formation methods. 7) Explored the mechanism of PCW to promote diabetic wound healing by protein blotting and immunohistochemical detection of relevant protein expression.

RESULTS

and finally: 1) After the above screening, 81 active ingredients of PCW and 94 targets acting on diabetic ulcers were obtained. 2) 30 biological processes, 30 cellular compositions and 30 molecular functions were obtained by GO analysis; 28 signaling pathways were obtained by KEGG analysis. 3) The results of AO/EB staining assay, scratch assay and in vitro tube-forming assay showed that PCW has significant pro-vascular endothelial cell proliferation and pro-angiogenic effects in vitro.

CONCLUSIONS

The results of this study confirmed the effect of the PCW in treating diabetic ulcers to a certain extent, and further revealed its mechanism of action in depth, which provides a new reference for the next step of Chinese medicine in treating diabetic ulcers.

Analysis of Effects of Surface Roughness on Sensing Performance of Surface Plasmon Resonance Detection for Refractive Index Sensing Application

This paper provides a theoretical framework to analyze and quantify roughness effects on sensing performance parameters of surface plasmon resonance measurements. Rigorous coupled-wave analysis and the Monte Carlo method were applied to compute plasmonic reflectance spectra for different surface roughness profiles. The rough surfaces were generated using the low pass frequency filtering method. Different coating and surface treatments and their reported root-mean-square roughness in the literature were extracted and investigated in this study to calculate the refractive index sensing performance parameters, including sensitivity, full width at half maximum, plasmonic dip intensity, plasmonic dip position, and figure of merit. Here, we propose a figure-of-merit equation considering optical intensity contrast and signal-to-noise ratio. The proposed figure-of-merit equation could predict a similar refractive index sensing performance compared to experimental results reported in the literature. The surface roughness height strongly affected all the performance parameters, resulting in a degraded figure of merit for surface plasmon resonance measurement.

Ligand binding constants for human serum albumin evaluated by ratiometric analysis of DSC thermograms

This paper describes an expanded application of our recently reported method (Eskew et al., Analytical Biochemistry 621,1 2021) utilizing thermogram signals for thermal denaturation measured by differential scanning calorimetry. Characteristic signals were used to quantitatively evaluate ligand binding constants for human serum albumin. In our approach the ensemble of temperature dependent calorimetric responses for various protein-ligand mixtures and native HSA were compared, in a ratiometric manner, to extract binding constants and stoichiometries. Protein/ligand mixtures were prepared at various ligand concentrations and subjected to thermal denaturation analysis by calorimetry. Measurements provided the melting temperature, T_m, and free-energy ΔG_cal(37°C) for melting ligand-bound Albumin as a function of ligand concentration. Concentration dependent behaviors of these parameters derived from protein/ligand mixtures were used to construct dose-response curves. Fitting of dose-response curves yielded quantitative evaluation of the ligand binding constant and semi-quantitative estimates of the binding stoichiometry. Many of the ligands had known binding affinity for Albumin with binding constants reported in the literature. Evaluated binding parameters for the ligands impressively agreed with reported literature values determined using other standard experimental methods. Results are reported for 29 drug ligands binding to Albumin. These validate our calorimetry-based process for applications in pre-clinical drug screening.

Multivalent Probes in Molecular Imaging: Reality or Future?

The rapidly developing field of molecular medical imaging focuses on specific visualization of (patho)physiological processes through the application of imaging agents (IAs) in multiple clinical modalities. Although our understanding of the principles underlying efficient IAs design has increased tremendously, many IAs still show poor in vivo imaging performance because of low binding affinity and/or specificity. These limitations can be addressed by taking advantage of multivalency, in which multiple copies of a ligand are employed to strengthen the interaction. We critically address specific challenges associated with the application of multivalent compounds in molecular imaging, and we give directions for a stepwise approach to the design of multivalent imaging probes to improve their target binding and pharmacokinetics (PK) for improved diagnostic potential.

Progress of tubulin polymerization activity detection methods

Tubulin, an important target in tumor therapy, is one of the hotspots in the field of antineoplastic drugs in recent years, and it is of great significance to design and screen new inhibitors for this target. Natural products and chemical synthetic drugs are the main sources of tubulin inhibitors. However, due to the variety of compound structure types, it has always been difficult for researchers to screen out polymerization inhibitors with simple operation, high efficiency and low cost. A large number of articles have reported the screening methods of tubulin inhibitors and their biological activity. In this article, the biological activity detection methods of tubulin polymerization inhibitors are reviewed. Thus, it provides a theoretical basis for the further study of tubulin polymerization inhibitors and the selection of methods for tubulin inhibitors.

Recent progress in micro/nano biosensors for shellfish toxin detection

Shellfish toxins, as one kind of marine toxin, have attracted worldwide attention due to their severe threat to food safety and human health. Therefore, it is highly essential and urgent to develop a low-cost and convenient method to detect these toxins. With the rapid advance in microfabrication processes, micro/nano biosensors provide novel approaches to address this issue. In addition to their features of low cost, portability, easy operation, high efficiency and high bioactivity, micro/nano biosensors have great potential to realize on-the-spot, rapid detection of shellfish toxins. This review focuses on the most recent advances in the development of micro/nano biosensors for shellfish toxin detection. These biosensors are mainly classified into five categories according to their transducer detection principles, which include optical devices, electrochemical sensors, electrochemiluminescence, field-effect transistors, and acoustic devices. Sensor strategies, toxin analytes, biosensitive elements, coupling methods and field detection performance are highlighted to discuss the applications of shellfish toxin detection. With advances in sensor technology, biomaterials, microfabrication and miniaturized electronics, micro/nano biosensors applied to in-field fast detection of shellfish toxins are expected to play a critical role in food safety, environmental monitoring, and foreign trade in the foreseeable future. Finally, the current challenges and future development trends of micro/nano biosensors for shellfish toxin detection are discussed.

Evaluation of Water-Soluble Mannich Base Prodrugs of 2,3,4,5-Tetrahydroazepino[4,3-b]indol-1(6H)-one as Multitarget-Directed Agents for Alzheimer's Disease

Different Mannich base derivatives have been studied with the aim of addressing the poor aqueous solubility of the recently disclosed 6-phenethyl-2,3,4,5-tetrahydroazepino[4,3-b]indol-1(6H)-one (1), a human butyrylcholinesterase inhibitor (hBChE, IC₅₀ 13 nM) and protective agent in NMDA-induced neurotoxicity, in in vivo assays. The N-(4-methylpiperazin-1-yl)methyl derivative 2 c showed a 50-fold increase in solubility in pH 7.4-buffered solution, high stability in serum and (half-life >24 h) and rapid (<3 min) conversion to 1 at acidic pH. Although less active than 1, 2 c retained moderate hBChE inhibition (IC₅₀ =3.35 μM) and a significant protective effect against NMDA-induced neurotoxicity at 0.1 μM. Moreover, 2 c resulted a weaker serum albumin binder than 1, could pass the blood-brain barrier, and exerted negligible cytotoxicity on HepG2 cells. These findings suggest that 2 c could be a water-soluble prodrug candidate of 1 for oral administration or a slow-release injectable derivative in in vivoAlzheimer's disease models.

Development of a Graphene-Based Surface Plasmon Resonance Optical Sensor Chip for Potential Biomedical Application

The emergence of unintentional poisoning and uncontrolled vector diseases have contributed to sensor technologies development, leading to the more effective detection of diseases. In this study, we present the combination of graphene-based material with surface plasmon resonance technique. Two different graphene-based material sensor chips were prepared for rapid and quantitative detection of dengue virus (DENV) and cobalt ion (Co2+) as an example of typical metal ions. As the fundamental concept of surface plasmon resonance (SPR) sensor that relies on the refractive index of the sensor chip surface, this research focused on the SPR signal when the DENV and Co2+ interact with the graphene-based material sensor chip. The results demonstrated that the proposed sensor-based graphene layer was able to detect DENV and Co2+ as low as 0.1 pM and 0.1 ppm respectively. Further details in the detection and quantification of analyte were also discussed in terms of sensitivity, affinity, and selectivity of the sensor.

Identification of eupatilin and ginkgolide B as p38 ligands from medicinal herbs by surface plasmon resonance biosensor-based active ingredients recognition system

Screening of bioactive ligands for a certain protein target from medicinal herbs is a highly important yet challenging task during drug discovery process. In this study, a surface plasmon resonance biosensor-based active ingredient recognition system (SPR-AIRS) was applied to screen p38 mitogen-activated protein kinase (p38) ligands from herbal extracts. After p38 protein was immobilized on a SPR chip and the suitability of SPR-AIRS was validated, thirty-four p38-related medicinal herbs were selected and pre-screened. Two medicinal herbs having high response signal with p38-immobilized chip, Folium Ginkgo and Herba Artemisiae Scopariae, were injected into SPR system for ligand fishing. Among them, two active compounds, eupatilin (EPT) and ginkgolide B (GKB), were identified as p38 ligands, and then the K_D values of EPT and GKB were measured as 21.68 ± 2.21 and 44.71 ± 1.80 μM, respectively. They can inhibit p38 activities significantly and bind to the ATP binding site on p38. Furthermore, EPT and GKB can inhibit cell proliferation (IC₅₀ = 30.31 ± 6.84 and 42.97 ± 0.83 μM), induce apoptosis and G2/M cell cycle arrest against K562 cell line. This is the first time that EPT and GKB are reported as effective p38 binding ligands. These results prove that SPR-AIRS could be an effective method to screen active compounds acting on a specific protein from complex systems.

Key Physicochemical Characteristics Influencing ADME Properties of Therapeutic Proteins

Therapeutic proteins are a rapidly growing class of drugs in clinical settings. The pharmacokinetics (PK) of therapeutic proteins relies on their absorption, distribution, metabolism, and excretion (ADME) properties. Moreover, the ADME properties of therapeutic proteins are impacted by their physicochemical characteristics. Comprehensive evaluation of these characteristics and their impact on ADME properties are critical to successful drug development. This chapter summarizes all relevant physicochemical characteristics and their effect on ADME properties of therapeutic proteins.

Thermophoresis for characterizing biomolecular interaction

The study of biomolecular interactions is crucial to get more insight into the biological system. The interactions of protein-protein, protein-nucleic acids, protein-sugars, nucleic acid-nucleic acids and protein-small molecules are supporting therapeutics and technological developments. Recently, the development in a large number of analytical techniques for characterizing biomolecular interactions reflect the promising research investments in this field. In this review, microscale thermophoresis technology (MST) is presented as an analytical technique for characterizing biomolecular interactions. Recent years have seen much progress and several applications established. MST is a powerful technique in quantitation of binding events based on the movement of molecules in microscopic temperature gradient. Simplicity, free solutions analysis, low sample volume, short analysis time, and immobilization free are the MST advantages over other competitive techniques. A wide range of studies in biomolecular interactions have been successfully carried out using MST, which tend to the versatility of the technique to use in screening binding events in order to save time, cost and obtained high data quality.

A Sensitive and Stable Surface Plasmon Resonance Sensor Based on Monolayer Protected Silver Film

In this paper, we present a stable silver-based surface plasmon resonance (SPR) sensor using a self-assembled monolayer (SAM) as a protection layer and investigated its efficiency in water and 0.01 M phosphate buffered saline (PBS). By simulation, silver-based SPR sensor has a better performance in field enhancement and penetration depth than that of a gold-based SPR sensor, which are 5 and 1.4 times, respectively. To overcome the instability of the bare silver film and investigate the efficiency of the protected layer, the SAM of 11-mercapto-1-undecanol (MUD) was used as a protection layer. Stability experiment results show that the protected silver film exhibited excellent stability either in pure water or 0.01 M PBS buffer. The sensitivity of the silver-based SPR sensor was calculated to be 127.26 deg/RIU (refractive index unit), measured with different concentrations of NaCl solutions. Further, a very high refractive resolution for the silver-based SPR sensor was found to be 2.207 × 10⁻⁷ RIU, which reaches the theoretical limit in the wavelength of 632.8 nm for a SPR sensor reported in the literature. Using a mixed SAM of 16-mercaptohexadecanoic acid (MHDA) and a MUD layer with a ratio of 1:10, this immunosensor for the rabbit immunoglobulin G (IgG) molecule with a limit of detection as low as 22.516 ng/mL was achieved.