Efficient Binding Research Articles

1,4-Pyrazolyl-Containing SAFit-Analogues are Selective FKBP51 Inhibitors With Improved Ligand Efficiency and Drug-Like Profile.

The FK506 binding protein 51 (FKBP51) is an appealing drug target due to its role in several diseases such as depression, anxiety, chronic pain and obesity. Towards this, selectivity versus the close homolog FKBP52 is essential. However, currently available FKBP51-selective ligands such as SAFit2 are too large and lack drug-like properties. Here, we present a structure activity relationship (SAR) analysis of the pipecolic ester moiety of SAFit1 and SAFit2, which culminated in the discovery of the 1,4-pyrazolyl derivative 23 d, displaying a binding affinity of 0.077 μM for FKBP51, reduced molecular weight (541.7 g/mol), lower hydrophobicity (cLogP=3.72) and higher ligand efficiency (LE=0.25). Cocrystal structures revealed the importance of the 1,4- and 1,3,4- substitution patterns of the pyrazole ring versus the 1,4,5 arrangement.

Effects of continuous nitrate treatment of hypolimnion in a small, hypereutrophic lake

Continuous nitrate treatment is an innovative, nature-based and cost-effective restoration method that has been implemented in a small, hypereutrophic lake by redirecting the nitrate-rich waters of the lake's natural tributaries into its hypolimnion. The aim of this treatment is to increase the redox potential at the sediment-water interface in order to provide conditions for efficient phosphorus binding. To assess the effects of this treatment, studies of the physico-chemical and biological parameters of the lake waters were carried out before its application (PreNT – years 2005–2007), during its application (FullNT – 2008–July 2019), and in the period when installation was partly clogged (LimNT- August 2019–2021). The results show effective improvement of oxygenation of the hypolimnion during the treatment followed by a decrease of phosphorus concentration – a proxy of the reduced internal loading. Water quality gradually improved during the treatment. The periods of cyanobacterial blooms shortened in some years, and ceased in other years, and it was also manifested by the increase in the range of Secchi depth and a decrease in chlorophyll-a concentration. The share of eukaryotic algae in the phytoplankton increased. The method showed high resistance to disturbances in its functioning, because during two years of operation of one pipeline, only a slight deterioration of water quality was observed. This enables effective repair of the hypolimnion's supply of nitrates, without a sudden return to the pre-restoration state. Finally, the benefits and limitations of hypolimnetic nitrate treatment (with nitrate from natural sources) were discussed to facilitate the application of this method to other lakes.

Enhanced curcumin solubility in epichlorohydrin engineered β-Cyclodextrin copolymer for gastric maladies

The present work relates to a β-cyclodextrin based drug delivery system with epichlorohydrin as cross-linking agent, with higher binding efficiency of the drug curcumin and enhanced solubility of the curcumin in complex form when simulated in gastric fluid and increased sustained release of curcumin from complex for 2 h to act in gastric region. Although cross-linking with epichlorohydrin (EPC) is a process studied long time ago, however its use as a gastric solubility enhancer for curcumin has been studied for the first time. The synthesized polymer was well characterized by FT-IR, SEM, XRD, TGA and particle size analysis. The polymer enhanced the water solubility of curcumin by ∼ 800–850 times and the gastric solubility was increased by ∼ 1400–1500 times and acted as a sustained release system as verified by the pepsin inhibition studies which makes it a potential drug carrier for gastric specific drug targeting that can be a promising treatment for gastritis and gastric ulcers.

Integrating network pharmacology and computational biology to propose Yiqi Sanjie formula's mechanisms in treating NSCLC: molecular docking, ADMET, and molecular dynamics simulation.

Non-small cell lung cancer (NSCLC) remains a leading cause of cancer-related deaths globally. Current treatments often do not fully meet efficacy and quality of life expectations. Traditional Chinese medicine (TCM), particularly the Yiqi Sanjie formula, shows promise but lacks clear mechanistic understanding. This study addresses this gap by investigating the therapeutic effects and underlying mechanisms of Yiqi Sanjie formula in NSCLC. We utilized network pharmacology to identify potential NSCLC drug targets of the Yiqi Sanjie formula via the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. Compounds with favorable oral bioavailability and drug-likeness scores were selected. Molecular docking was conducted using AutoDock Vina with structural data from the Protein Data Bank and PubChem. Molecular dynamics (MD) simulations were performed with Desmond Molecular Dynamics System, analyzing interactions up to 500 nanoseconds using the OPLS4 force field. ADMET predictions were executed using SwissADME and ADMETlab 2.0, assessing pharmacokinetic properties. Using network pharmacology tools, we performed Search Tool for the Retrieval of Interaction Genes/Proteins (STRING) analysis for protein-protein interaction, Kyoto Encyclopedia of Genes and Genomes (KEGG) for pathway enrichment, and gene ontology (GO) for functional enrichment, identifying crucial signaling pathways and biological processes influenced by the hit compounds bifendate, xambioona, and hederagenin. STRING analysis indicated substantial connectivity among the targets, suggesting significant interactions within the cell cycle regulation and growth factor signaling pathways as outlined in our KEGG results. The GO analysis highlighted their involvement in critical biological processes such as cell cycle control, apoptosis, and drug response. Molecular docking simulations quantified the binding efficiencies of the identified compounds with their targets-CCND1, CDK4, and EGFR-selected based on high docking scores that suggest strong potential interactions crucial for NSCLC inhibition. Subsequent MD simulations validated the stability of these complexes, supporting their potential as therapeutic interventions. Additionally, the novel identification of ADH1B as a target underscores its prospective significance in NSCLC therapy, further expanded by our comprehensive bioinformatics approach. Our research demonstrates the potential of integrating network pharmacology and computational biology to elucidate the mechanisms of the Yiqi Sanjie formula in NSCLC treatment. The identified compounds could lead to novel targeted therapies, especially for patients with overexpressed targets. The discovery of ADH1B as a therapeutic target adds a new dimension to NSCLC treatment strategies. Further studies, both in vitro and in vivo, are needed to confirm these computational findings and advance these compounds towards clinical trials.

Dendrimer Platforms for Targeted Doxorubicin Delivery-Physicochemical Properties in Context of Biological Responses.

The unique structure of G4.0 PAMAM dendrimers allows a drug to be enclosed in internal spaces or immobilized on the surface. In the conducted research, the conditions for the formation of the active G4.0 PAMAM complex with doxorubicin hydrochloride (DOX) were optimized. The physicochemical properties of the system were monitored using dynamic light scattering (DLS), circular dichroism (CD), and fluorescence spectroscopy. The Quartz Crystal Microbalance with Dissipation Monitoring (QCM-D) method was chosen to determine the preferential conditions for the complex formation. The highest binding efficiency of the drug to the cationic dendrimer was observed under basic conditions when the DOX molecule was deprotonated. The decrease in the zeta potential of the complex confirms that DOX immobilizes through electrostatic interaction with the carrier's surface amine groups. The binding constants were determined from the fluorescence quenching of the DOX molecule in the presence of G4.0 PAMAM. The two-fold way of binding doxorubicin in the structure of dendrimers was visible in the Isothermal calorimetry (ITC) isotherm. Fluorescence spectra and release curves identified the reversible binding of DOX to the nanocarrier. Among the selected cancer cells, the most promising anticancer activity of the G4.0-DOX complex was observed in A375 malignant melanoma cells. Moreover, the preferred intracellular location of the complexes concerning the free drug was found, which is essential from a therapeutic point of view.

Acoustofluidics-enhanced biosensing with simultaneously high sensitivity and speed

Simultaneously achieving high sensitivity and detection speed with traditional solid-state biosensors is usually limited since the target molecules must passively diffuse to the sensor surface before they can be detected. Microfluidic techniques have been applied to shorten the diffusion time by continuously moving molecules through the biosensing regions. However, the binding efficiencies of the biomolecules are still limited by the inherent laminar flow inside microscale channels. In this study, focused traveling surface acoustic waves were directed into an acoustic microfluidic chip, which could continuously enrich the target molecules into a constriction zone for immediate detection of the immune reactions, thus significantly improving the detection sensitivity and speed. To demonstrate the enhancement of biosensing, we first developed an acoustic microfluidic chip integrated with a focused interdigital transducer; this transducer had the ability to capture more than 91% of passed microbeads. Subsequently, polystyrene microbeads were pre-captured with human IgG molecules at different concentrations and loaded for detection on the chip. As representative results, ~0.63, 2.62, 11.78, and 19.75 seconds were needed to accumulate significant numbers of microbeads pre-captured with human IgG molecules at concentrations of 100, 10, 1, and 0.1 ng/mL (~0.7 pM), respectively; this process was faster than the other methods at the hour level and more sensitive than the other methods at the nanomolar level. Our results indicated that the proposed method could significantly improve both the sensitivity and speed, revealing the importance of selective enrichment strategies for rapid biosensing of rare molecules.

Synthesis of mannose conjugated biodegradable polyester-based nanocarriers and their binding study with Concanavalin A

In this paper, we aim to create fully biodegradable glyconanoparticles formed via self-assembly of glycopolymers, comprising of biodegradable aliphatic polyester conjugated with mannose moiety. To accomplish the goal, a series of random copolymers comprised of poly(propargyl glycolide-co-lactide) were synthesized. Alkyne moiety of the poly (propargyl glycolide) component was then clicked with mannose ethyl azide to produce amphiphilic glycopolymers in good yield (60–75 %). The glycopolymers were then self-assembled to form glyconanoparticles of 15–23 nm size in dry state and 78–88 nm size in hydrated state (hydrodynamic diameter). The copolymers were characterized by NMR and FTIR, whereas the nanoparticles were thoroughly characterized by DLS, FESEM, and HR-TEM and explored for their lectin binding efficiency. Isothermal calorimetry (ITC) experiments suggest a stronger binding efficiency of glyconanoparticles towards mannose-specific lectin such as Concanavalin A, as compared to its corresponding glycopolymers (∼2 fold) and monomeric mannose unit (∼7-fold) as well. Moreover, curcumin was selected as the model drug to be encapsulated (∼76 % encapsulation efficiency) and released (74 % in 24 h) from the glyconanoparticles. Apart from these, excellent haemocompatibility, cell viability, and cellular uptake of the nanoparticles (more than 80 % cells showed uptake of the nanoparticles), further supported their potential as drug carriers having sugar as a targeting moiety.

Highly Electroactive Co2+-Based Metal-Organic Frameworks as an Efficient Coreaction Accelerator for Amplifying Near-Infrared Electrochemiluminescence of Gold Nanoclusters in Biomarkers Immunoassay.

Metal nanoclusters (NCs) as a new kind of luminophore have acquired sufficient interest, but their widespread application is restricted on account of their relatively low electrochemiluminescence (ECL) efficiency. Then, aqueous metal NCs with high ECL efficiency were strongly anticipated, especially for the ultrasensitive analysis of biomarkers. Herein, a near-infrared (NIR) ECL biosensing strategy for the test of neuron-specific enolase (NSE) was proposed by utilizing N-acetyl-l-cysteine (NAC)- and cysteamine (Cys)-stabilized gold NCs (NAC/Cys-AuNCs) as ECL emitters with the NIR ECL emission around 860 nm and a metal-organic framework/palladium nanocubes (ZIF-67/PdNCs) hybrid as the coreaction accelerator through their admirable electrocatalytic activity. The NIR emission would reduce photochemical injury to the samples and even realize nondestructive analysis with highly strong susceptibility and suitability. Furthermore, the utilization of ZIF-67/PdNCs could improve the ECL response of NAC/Cys-AuNCs by facilitating the oxidation of the coreactant triethylamine (TEA), leading to the production of a larger quantity of reducing intermediate radical TEA•+. Consequently, NAC/Cys-AuNCs with ZIF-67/PdNCs displayed 2.7 fold enhanced ECL emission compared with the single NAC/Cys-AuNCs using TEA as the coreactant. In addition, HWRGWVC (HWR), a heptapeptide, was introduced to immobilize antibodies for the specially binding Fc fragment of the antibodies, which improved the binding efficiency and sensitivity. As a result, a "signal-on" immunosensor for NSE analysis was obtained with an extensive linear range of 0.1 to 5 ng/mL and a low limit of detection (0.033 fg/mL) (S/N = 3). This study provides a wonderful method for the development of an efficient nondestructive immunoassay.

Hemoglobin Hydrolyzate Promotes Iron Absorption in the Small Intestine through Iron Binding Peptides.

Hemoglobin is an excellent source of iron supplements, and its hydrolyzate spontaneously binds iron during digestion and promotes iron absorption in vivo. However, the underlying mechanisms of what peptides bind and how they bind iron ions remain unclear. This study prepared the porcine hemoglobin hydrolyzate through enzymatic hydrolysis and acid treatment and investigated the mechanisms of hemoglobin hydrolyzate on iron absorption through the determination of iron levels in dietary intervention mice, iron binding site analyses, peptide digestion analyses, molecular simulation docking, and INT407 cell validation. The results showed that ingestion of the hemoglobin hydrolyzate diets increased iron levels in the blood of mice, accompanied by the upregulation of duodenal iron circulation-related genes such as ferritin, PCBP1, and HP. Carboxyl, imidazole groups, and aromatic amino acid residues were iron binding sites of hemoglobin hydrolyzate during digestion. VDEVGGEA and VDEVGGE were found to involve the spontaneous and efficient binding of hemoglobin hydrolyzate to iron ions in the intestinal cavity. In particular, the DEVGGE peptide was the typical sequence for hemoglobin hydrolytic peptides to exert iron binding activity.

A theoretical approach on ADMET properties of an azo-ester based fluorophore (AEF), and it's energetics, binding stability and molecular interactions with select globular proteins

Molecular docking (Mol.Doc) approach of an azo-ester based fluorophore (AEF) with widely studied proteins like Human serum Albumin (HSA), Bovine serum Albumin (BSA), Beta lactoglobin (βLG) and Ovalbumin (OVA) were carried out. The binding affinity and strength of AEF-HSA complex is due to hydrogen-bonding (h-bonding) and hydrophobic interactions (predominantly attributed to pi-alkyl). AEF and HSA acts as h-bonding acceptor as well as donor. The energetically favored conformers of AEF-HSA complex are governed and stabilized by polar as well as non-polar amino acids. On the contrary, the pattern observed in all the conformers of AEF-BSA, AEF- βLG and AEF-OVA are energetically least favored (+ve ∆G) compared to that of HSA. The least binding affinity of AEF is towards OVA (Binding energy (BE) +581.15 Kcalmol−1 followed by βLG (+55.11) and BSA (+12.12) . Though BSA and HSA are structurally similar to each other, they vary in the binding stability with AEF. This is attributed to several unfavorable interactions that destabilize AEF-BSA complex which was not resulted in the complex existing between AEF-HSA. The energetically least stable complexes (AEF-BSA, AEF-βLG and AEF-OVA) are predominantly governed by hydrophobic interactions. However, several h-bonding interactions along with pi-sigma/pi-pi/pi-alkyl interactions result in destabilization of the above complexes. Interestingly, AEF-HSA complex stability is attributed to fewer number of hydrophobic interactions along with h-bonding interactions. The h-bonding interaction governs the stability of the complex which is the driving force. Docking studies illustrates that the binding of amino acids (AAs) in various subdomains play a significant role on the binding nature. The stability of AEF-HSA over other protein complexes in terms of BE is emphasized in the study. The energetically stable sites and sub-domains of AEF with HSA and BSA establish the site selective and site-specific nature of AEF with proteins. In silico studies provide an excellent and easier approach in establishing the molecular interactions existing between AEF with globular proteins. ADMET parameters of the guest molecule calculated exemplifies that AEF compound is less toxic and possesses high oral bioavailability. Based on the binding efficiency of AEF with albumins, the ADMET properties and drug likeliness approach of AEF provides an information on the application towards proteins in the concept of medicine and chemistry.

Synthesis and characterization of newly phthalocyanine molecules: Their enzyme inhibition and antioxidant properties, in silico and in vitro

Pcs exhibiting maximum absorption in the phototherapeutic window continue to shine as a beacon of hope in the treatment of cancer. In particular, they maintain skin sensitivity after treatment and can treat deep-seated tumors by stimulating them with broad-spectrum radiation. This makes them advantageous compared to their counterparts. In this study, Novel 1,2,3-triazole schiff base (5a), its methoxy homolog (5b), and their silicon complexes (SiPc-6a and SiPc-6b) were synthesized. Their proposed structures were confirmed by FT-IR, NMR, UV–vis and MS instrumental techniques. Compound (6b) showed inhibitory activity on amylase and glucosidase enzymes. Moreover, considering the glucosidase activity, compound (6b) (IC50, 22.4 ± 1.0 µM) was observed to be more effective than the standard compound (IC50, 186.1 ± 5.8 µM). Molecular docking studies showed that the synthesized compounds bind to the same enzymes with high affinity. The binding energy of SiPc-6a compound with α-amylase, α-glucosidase and tyrosinase enzymes are -10.28, -11.31 and -11.9 kcal/mol, respectively. And another compound, SiPc-6b, has a binding energy of -11.46, -10.11 and -10.27 kcal/mol with a-amylase, a-glucosidase and tyrosinase enzymes, respectively. Based on experimental results that support each other with binding energy values in quality and quantity indicating efficient binding, it is concluded that these compounds can be used in candidate drug discovery. Beside these, as a result of the studies, it was understood that all molecules have antioxidant activity. Additionally, molecular electrostatic potentials, frontier orbital analysis, natural bond orbital (NBO) properties of compounds calculated with DFT and TD-DFT methods and these properties associated with structural properties.

Graphene oxide-supported molybdenum complex as catalyst for peroxidase and catechol oxidase-like reactions

In this study, we synthesized a molybdenum complex, [MoO2(L)(H2O)] (1), utilizing a Schiff base ligand H2L (I), which was formed by reacting 3,5-di-tert-butyl-2-hydroxybenzaldehyde with the mono hydrazide of terephthalic ester in a methanolic solution. This complex was subsequently immobilized on a functionalized graphene oxide surface (APTES@GO), prepared using 3-aminopropyltriethoxysilane (APTES) and graphene oxide (GO), yielding the supported complex [MoO2(L)(H2O)]@APTES@GO (2). Both complexes were characterized through various analytical techniques, with single-crystal X-ray diffraction (SC-XRD) being specifically employed for complex 1. The catalytic activities of the homogeneous and heterogeneous complexes were assessed for their peroxidase-like and catechol oxidase-like functions, particularly in the oxidation of 3,3′-diaminobenzidine (DAB) and 3,5-di-tert-butylcatechol (3,5-DTBC) in the presence of hydrogen peroxide. Both complexes exhibited excellent catalytic efficiency (Kcat) and substrate binding affinity (KM), comparable to natural enzymes. Additionally, the supported complex demonstrated good reusability, maintaining its catalytic activity over five consecutive cycles.

Antibody-Driven Assembly of Plasmonic Core-Satellites to Increase the Sensitivity of a SERS Vertical Flow Immunoassay.

Here, we describe a SERS-based vertical flow assay as a platform technology suitable for point-of-care (POC) diagnostic testing. A capture substrate is constructed from filter paper embedded with spherical gold nanoparticles (AuNPs) and functionalized with an appropriate capture antibody. The capture substrate is loaded into a filtration device and connected to a syringe to rapidly and repeatedly pass the sample through the sensor for efficient antigen binding. The antigen is then labeled with a SERS-active detection probe. We show that only a few Raman reporter molecules, exclusively located adjacent to the plasmonic capture substrate, generate detectible signals. To maximize the signal from underutilized Raman reporter molecules, we employ a secondary signal enhancing probe that undergoes antibody-directed assembly to form plasmonic core-satellites. This facile enhancement step provides a 3.5-fold increase in the signal and a detection limit of 0.23 ng/mL (1.6 pM) for human IgG. This work highlights the potential to rationally design plasmonic architectures using widely available and reproducible spherical AuNPs to achieve large SERS enhancements for highly sensitive POC diagnostics.

The surface modification of the silica-coated magnetic nanoparticles and their application in molecular diagnostics of virus infection

The study presents a series of examples of magnetic nanoparticle systems designed for the diagnosis of viral diseases. In this interdisciplinary work, we describe one of the most comprehensive synthetic approaches for the preparation and functionalization of smart nanoparticle systems for rapid and effective RT-PCR diagnostics and isolation of viral RNA. Twelve different organic ligands and inorganic porous silica were used for surface functionalization of the Fe3O4 magnetic core to increase the number of active centres for efficient RNA binding from human swab samples. Different nanoparticle systems with common beads were characterized by HRTEM, SEM, FT-IR, XRD, XPS and magnetic measurements. We demonstrate the application of the fundamental models modified to fit the experimental zero-field cooling magnetization data. We discuss the influence of the nanoparticle shell parameters (morphology, thickness, ligands) on the overall magnetic performance of the systems. The prepared nanoparticles were tested for the isolation of viral RNA from tissue samples infected with hepatitis E virus—HEV and from biofluid samples of SARS-CoV-2 positive patients. The efficiency of RNA isolation was quantified by RT-qPCR method.

Capture and Storage of Cell-Free DNA via Bio-Informational Hydrogel Microspheres.

Excessive cell-free DNA (cfDNA) can induce chronic inflammation by activating intracellular nucleic acid sensors. Intervention in cfDNA-mediated "pro-inflammatory signaling transduction" could be a potential alleviating strategy for chronic inflammation, such as in diabetic wounds. However, effectively and specifically downgrading cfDNA concentration in the pathological microenvironment remains a challenge. Therefore, this work prepares free-standing polydopamine nanosheets through DNA-guided assembly and loaded them into microfluidic hydrogel microspheres. The π─π stacking/hydrogen bonding interactions between polydopamine nanosheets and the π-rich bases of cfDNA, along with the cage-like spatial confinement created by the hydrogel polymer network, achieved cfDNA capture and storage, respectively. Catechol in polydopamine nanosheets can also assist in reducing reactive oxygen species (ROS) levels. Efficient cfDNA binding independent of serum proteins, specific interdiction of abnormal activation of cfDNA-associated toll-like receptor 9, as well as down-regulation of inflammatory cytokines and ROS levels are shown in this system. The chronic inflammation alleviating and the pro-healing effects on the mice model with diabetic wounds are also investigated. This work presents a new strategy for capturing and storing cfDNA to intervene in cell signaling transduction. It also offers new insights into the regulatory mechanisms between inflammatory mediators and biomaterials in inflammation-related diseases.

PxBLAT: an efficient python binding library for BLAT

BackgroundWith the surge in genomic data driven by advancements in sequencing technologies, the demand for efficient bioinformatics tools for sequence analysis has become paramount. BLAST-like alignment tool (BLAT), a sequence alignment tool, faces limitations in performance efficiency and integration with modern programming environments, particularly Python. This study introduces PxBLAT, a Python-based framework designed to enhance the capabilities of BLAT, focusing on usability, computational efficiency, and seamless integration within the Python ecosystem.ResultsPxBLAT demonstrates significant improvements over BLAT in execution speed and data handling, as evidenced by comprehensive benchmarks conducted across various sample groups ranging from 50 to 600 samples. These experiments highlight a notable speedup, reducing execution time compared to BLAT. The framework also introduces user-friendly features such as improved server management, data conversion utilities, and shell completion, enhancing the overall user experience. Additionally, the provision of extensive documentation and comprehensive testing supports community engagement and facilitates the adoption of PxBLAT.ConclusionsPxBLAT stands out as a robust alternative to BLAT, offering performance and user interaction enhancements. Its development underscores the potential for modern programming languages to improve bioinformatics tools, aligning with the needs of contemporary genomic research. By providing a more efficient, user-friendly tool, PxBLAT has the potential to impact genomic data analysis workflows, supporting faster and more accurate sequence analysis in a Python environment.

Synthesis and biological characterization of an orally bioavailable lactate dehydrogenase-A inhibitor against pancreatic cancer

Lactate dehydrogenase-A (LDHA) is the major isoform of lactate dehydrogenases (LDH) that is overexpressed and linked to poor survival in pancreatic ductal adenocarcinoma (PDAC). Despite some progress, current LDH inhibitors have poor structural and physicochemical properties or exhibit unfavorable pharmacokinetics that have hampered their development. The present study reports the synthesis and biological evaluation of a novel class of LDHA inhibitors comprising a succinic acid monoamide motif. Compounds 6 and 21 are structurally related analogs that demonstrated potent inhibition of LDHA with IC50s of 46 nM and 72 nM, respectively. We solved cocrystal structures of compound 21-bound to LDHA that showed that the compound binds to a distinct allosteric site between the two subunits of the LDHA tetramer. Inhibition of LDHA correlated with reduced lactate production and reduction of glycolysis in MIA PaCa-2 pancreatic cancer cells. The lead compounds inhibit the proliferation of human pancreatic cancer cell lines and patient-derived 3D organoids and exhibit a synergistic cytotoxic effect with the OXPHOS inhibitor phenformin. Unlike current LDHA inhibitors, 6 and 21 have appropriate pharmacokinetics and ligand efficiency metrics, exhibit up to 73% oral bioavailability, and a cumulative half-life greater than 4 h in mice.

Inhibition of RNA Phosphodiester Backbone Cleavage in the Presence of Organic Cations of Different Sizes.

Living cells contain various types of organic cations that may interact with nucleic acids. In order to understand the nucleic acid-binding properties of organic cations of different sizes, we investigated the ability of simple organic cations to inhibit the RNA phosphodiester bond cleavage promoted by Mg2+, Pb2+, and RNA-cleaving serum proteins. Kinetic analysis using chimeric DNA-RNA oligonucleotides showed that the cleavage at ribonucleotide sites was inhibited in the presence of monovalent cations comprising alkyl chains or benzene rings. The comparison of the cleavage rates in the presence of quaternary ammonium and phosphonium ions indicated that the steric hindrance effect of organic cations on their binding to the RNA backbone is significant when the cation size is larger than the phosphate-phosphate distance of a single-stranded nucleic acid. The cleavage inhibition was also observed for ribonucleotides located in long loops but not in short loops of oligonucleotide structures, indicating less efficient binding of bulky cations to structurally constrained regions. These results reveal the unique nucleic acid-binding properties of bulky cations distinct from those of metal ions.

New insights into how freeze-drying and cryo-milling affects the fine structure and digestibility of gelatinized starch

Freeze-drying (FD) and cryo-milling (CM) are common methods for preparing powder gelatinized starch samples. This study investigates the structural characterization of raw/gelatinized maize starches and digestibility after FD/CM processes to elucidate their effect on starch digestibility determination. Results showed that FD slightly increased digestibility, while higher initial glucose content in CM samples, especially for gelatinized samples. Only FD retained the granular morphology and relative crystallinity (RC), while gelatinized-FD decreased RC by 75%. CM decreased RC by 12%, while gelatinized-CM decreased it by 97%. Combined with short-range and chain structural results, FD tended to disrupt internal connected chains through volume stress, while CM cleaved glycosidic bonds in external chain. Stretched chains in gelatinized starch promoted the breakage of chains during shearing and their efficient binding with digestive enzymes. These findings would provide a basis for pre-treatment of powder samples and processes of starch- rich foods.

The influence of various polymer coatings on the in vitro and in vivo properties of PLGA nanoparticles: Comprehensive study

Nanoparticles based on poly(lactic-co-glycolic acid) (PLGA) with various surface chemistry are widely used in biomedicine for theranostic applications. The nature of the external coating of nanoparticles has a significant influence on their efficiency as drug carriers or visualization agents. However, information about the mechanisms of nanoparticle accumulation in tumors and the influence of their surface properties on biodistribution is scarce due to the lack of systematic evaluation. Here we investigate the effect of different polymer coatings of the surface on in vitro and in vivo properties of PLGA nanoparticles. Namely, cell binding efficiency, cytotoxicity, efficiency of fluorescent bioimaging, and tumor accumulation were tested. The highest binding efficiency in vitro and cytotoxicity were observed for positively charged polymers. Interestingly, in vivo fluorescent visualization of tumor-bearing mice and quantitative measurements of biodistribution of magnetite-loaded nanoparticles indicated different dependences of accumulation in tumors on the coating of PLGA nanoparticles. This means that nanoparticle surface properties can simultaneously enhance imaging efficiency and decrease quantitative accumulation in tumors. The obtained data demonstrate the complexity of the dependence of nanoparticles’ effectiveness for theranostic applications on surface features. We believe that this study will contribute to the rational design of nanoparticles for effective cancer diagnostics and therapy.