High Affinity Binding Research Articles

RNA binding tunes the conformational plasticity and intradomain stability of TDP-43 tandem RNA recognition motifs

TAR DNA binding protein 43 (TDP-43) is a nuclear RNA/DNA-binding protein with pivotal roles in RNA-related processes such as splicing, transcription, transport, and stability. The high binding affinity and specificity of TDP-43 toward its cognate RNA sequences (GU-rich) is mediated by highly conserved residues in its tandem RNA recognition motif (RRM) domains (aa: 104–263). Importantly, the loss of RNA binding to the tandem RRMs caused by physiological stressors and chemical modifications promotes cytoplasmic mislocalization and pathological aggregation of TDP-43. Despite the substantial implications of RNA binding in TDP-43 function and pathology, its precise effects on the intradomain stability, and conformational dynamics of the tandem RRMs is not properly understood. Here, we employed all-atom molecular dynamics (MD) simulations to assess the effect of RNA binding on the conformational landscape and intradomain stability of TDP-43 tandem RRMs. RNA limits the overall conformational space of the tandem RRMs and promotes intradomain stability through a combination of specific base stacking interactions and transient electrostatic interactions. In contrast, tandem RRMs exhibit a high intrinsic conformational plasticity in the absence of RNA, which, surprisingly, is accompanied by a tendency of RRM1 to adopt partially unfolded conformations. Overall, our simulations reveal how RNA binding dynamically tunes the structural and conformational landscape of TDP-43 tandem RRMs, contributing to physiological function and mitigating pathological aggregation.

In silico Investigation of Caged Xanthone Compounds Isolated from Cratoxylum sumatranum Stem Bark against Entamoeba histolytica Enzymes

Background: Amoebiasis is caused by Entamoeba histolytica, a pathogenic species living on human colon tissues. Metronidazole is currently used for the treatment of amoebiasis, but resistance of E. histolytica to the use of such treatment has been reported. Therefore, the development of new anti-amoebic drugs is still very much needed for clinical treatment. Preliminary research on extract and fractions from Cratoxylum sumatranum stem bark has shown their anti-amoebic activity. Two compounds from the cage xanthone groups, cochinchinoxanthone and cochinchinone D, have been isolated from the active fraction of C. sumatranum stem bark. Objective: This study aimed to investigate the anti-amoebic activity of the two known compounds against E. histolytica. Methods: The in silico method used was molecular docking with several receptors, including thioredoxin reductase, triose phosphate isomerase, pyruvate ferredoxin oxidoreductase, Giardia fructose-1,6-bisphosphate aldolase, serine acetyltransferase, and phosphoserine phosphatase. The prediction of ADMET properties was also carried out for both the compounds. Results: The results showed cochinchinone D to have a higher binding affinity to thioredoxin reductase, pyruvate ferredoxin oxidoreductase, and Giardia fructose-1,6-bisphosphate aldolase receptors than cochinchinoxanthone. In contrast, cochinchinoxanthone bound better to the triose phosphate isomerase and phosphoserine phosphatase receptors, while both exhibited the same affinity for serine acetyltransferase. In general, the two compounds were also found to have similar ADMET profiles. Conclusion: In conclusion, caged xanthone compounds from C. sumatranum have the potential to be developed as anti-amoebic agents against E. histolytica through the mechanism of inhibition of these enzymes.

Potent Small Molecules Inhibitors Discovery through Ligand-based Modelling for Effective Treatment of Parkinson’s Disease

Background: Parkinson’s disease (PD) is a chronic neurodegenerative disease affecting mostly aged people. The disease's symptoms develop gradually over time and include tremors, bradykinesia, rigidity, and postural instability. Current treatment options for PD are only symptom-targeted. Prolyl oligopeptidase (POP) is a serine protease enzymes implicated in PD pathogenesis via an increase in the aggregation of α-synuclein protein in the brain. Aim: This study aims to identify potent anti-PD ligands with inhibitory potential against POP Methods: Ligand-based pharmacophore modeling, Glide extra precision (XP) docking, and post-simulation analysis methods were used. Results: The adopted ligand-based (LB) modeling generated pharmacophoric features, including 1 hydrophobic group, 1 positive ionizable group, 2 aromatic rings, and 2 hydrogen bond acceptors. A total of 23 hits with a Gunner-Henry score of 0.7 and an enrichment factor of 30.24 were obtained as validation protocols, making it an ideal model. The LB model retrieved 177 hit compounds from the 69,543 natural screening ligands available in the Interbioscreen database. Interestingly, ligands 1, 2, 3, 4, and 5 orderly demonstrated higher binding affinities with Glide XP docking of -9.0, -8.8, -8.7, -8.7, -8.7 kcal/mol compared to reference drugs, GSK552 and ZPP with -8.2, and -6.8 kcal/mol respectively. Similarly, their MM/GBSA values were recorded as -54.4, -51.3, -58.4, -49.3, - 33.5, & -32.5 kJ/mol respectively. Further, MD analysis indicated that ligands had higher favorable binding and stability to the receptor. Conclusion: Overall, the study paves the way for developing potential anti-PD therapeutics. The ligands are recommended as adjuvant/single candidate as anti-PD candidates upon further experiment.

PH-responsive chiral supramolecular cysteine-Zn2+-indocyanine green assemblies for triple-level chirality-specific anti-tumor efficacy

Chirality, ubiquitous in living matter, plays vital roles in a series of physiological processes. The clarification of the multiple functions of chirality in bioapplications may provide innovative methodologies for engineering anti-tumor agents. Nevertheless, the related research has been rarely explored. In this study, the chiral supramolecular l/d-cysteine (Cys)-Zn2+-indocyanine green (ICG) nanoparticles were constructed through the coordination interaction between l/d-Cys and Zn2+, followed by the encapsulation of ICG. Experimental findings revealed that the l/d-Cys-Cys-Zn2+-ICG exhibited 17.31 times higher binding affinity toward phospholipid-composed liposomes compared to l-Cys-Zn2+-ICG. Furthermore, driven by chirality-specific interaction, a 2.07 folds greater cellular internalization of d-Cys-Zn2+-ICG than l-Cys-Zn2+-ICG was demonstrated. Additionally, the triple-level chirality-dependent photothermal, photodynamic and Zn2+ releasing anti-tumor effects of l/d Cys-Zn2+-ICG in vitro were verified. As a result, the d-formed nanoparticles achieved 1.93 times higher anti-tumor efficiency than the l-formed ones. The triple-level chirality-mediated anti-tumor effect highlighted in this study underscores the enormous potential of chirality in biomedicine and holds substantial significance in improving cancer therapeutic efficacy.

Antibacterial activity of Au(I), Pt(II), and Ir(III) biotin conjugates prepared by the iClick reaction: influence of the metal coordination sphere on the biological activity.

A series of biotin-functionalized transition metal complexes was prepared by iClick reaction from the corresponding azido complexes with a novel alkyne-functionalized biotin derivative ([Au(triazolatoR,R')(PPh3)], [Pt(dpb)(triazolatoR,R')], [Pt(triazolatoR,R')(terpy)]PF6, and [Ir(ppy)(triazolatoR,R')(terpy)]PF6 with dpb = 1,3-di(2-pyridyl)benzene, ppy = 2-phenylpyridine, and terpy = 2,2':6',2''-terpyridine and R = C6H5, R' = biotin). The complexes were compared to reference compounds lacking the biotin moiety. The binding affinity toward avidin and streptavidin was evaluated with the HABA assay as well as isothermal titration calorimetry (ITC). All compounds exhibit the same binding stoichiometry of complex-to-avidin of 4:1, but the ITC results show that the octahedral Ir(III) compound exhibits a higher binding affinity than the square-planar Pt(II) complex. The antibacterial activity of the compounds was evaluated on a series of Gram-negative and Gram-positive bacterial strains. In particular, the neutral Au(I) and Pt(II) complexes showed significant antibacterial activity against Staphylococcus aureus and Enterococcus faecium at very low micromolar concentrations. The cytotoxicity against a range of eukaryotic cell lines was studied and revealed that the octahedral Ir(III) complex was non-toxic, while the square-planar Pt(II) and linear Au(I) complexes displayed non-selective micromolar activity.

Preclinical Development of SHR-1819, a Potent Humanized IL-4Rα Antibody for Treating Type 2 Inflammatory Diseases.

Interleukin (IL)-4 and IL-13 are critical pathogenic factors for type 2 inflammation-related allergic diseases, sharing the mutual receptor subunit IL-4Rα. However, it was ineffective for certain type 2 inflammation diseases by targeting IL-4, IL-13 ligand alone or both in clinical studies. The work presented herein aimed to evaluate the preclinical efficacy and pharmacokinetics profile of a novel monoclonal antibody against IL-4Rα, SHR-1819, as a promising therapy for type 2 inflammation diseases. SHR-1819 was generated through immunization by C57BL/6 mice with recombinant hIL-4Rα protein, followed by humanization and affinity maturation. Then, its binding properties with IL-4Rα were determined using surface plasmon resonance (SPR) and ELISA. In vitro inhibitory effects of SHR-1819 were assessed on hIL-4-/hIL-13-induced cell proliferation and signal transducer and activator of transcription 6 (STAT6) signaling activation. In vivo efficacy of SHR-1819 was evaluated in several type 2 inflammatory diseases models, including asthma, atopic dermatitis (AD), and allergic rhinitis (AR) by using hIL-4/hIL-4Rα transgenic mice. Furthermore, the pharmacokinetic (PK) profiles of SHR-1819 were characterized. SHR-1819 showed high binding affinity to human IL-4Rα and effectively blocked IL-4Rα at sub-nanomolar concentration. In vitro assays indicated that SHR-1819 significantly inhibited TF-1 cell proliferation and STAT6 activation induced by hIL-4/hIL-13. In the asthma model, SHR-1819 could reduce airway hyperresponsiveness, decrease serum IgE levels, and alleviated inflammatory lung cell infiltration. In the AD model, SHR-1819 could significantly alleviate inflammatory and skin symptoms. In the AR model, it could remarkably decrease the frequencies of nasal rubbing and sneezing, and inflammatory cell infiltration in nasal tissues. These in vivo efficacy studies demonstrated the therapeutic potential of SHR-1819 in preclinical disease models. Moreover, subcutaneous administration of SHR-1819 exhibited favorable bioavailability in mice. The results supported SHR-1819 as a promising preclinical candidate for the treatment of type 2 inflammatory diseases, including asthma, AD and AR.

Natural flavonoids as promising lactate dehydrogenase A inhibitors: Comprehensive in vitro and in silico analysis.

The inhibitory potential of 17 flavonoids on lactate dehydrogenase A (LDHA), a key enzyme in the downstream process of aerobic glycolysis in cancer cells, is investigated. Fisetin exhibited excellent inhibitory activity (IC50 = 0.066 µM). Quercetin 3-β-D-glucoside, quercetin 3-galactoside, luteolin, neoeriocitrin, and luteolin 7-O-β-D-glucoside showed good inhibitory activity (IC50 = 1.397-15.730 µM). Biochanin A, baicalein, quercetin, scutellarein-7-glucuronide, diosmetin, baicalein 7-O-β-D-glucuronide, and apigenin 7-apioglucoside demonstrated moderate inhibitory activity (IC50 = 33.007-86.643 µM). Eriodictyol, quercetin 7-O-β-D-glucoside, apigenin 7-O-β-D-glucoside, and epicatechin were inactive. The Lineweaver-Burk plot showed that fisetin competitively inhibits NADH binding (Ki = 0.024 µM). Ki values for other compounds were calculated using the Cheng-Prusoff equation (Ki = 0.2799-2.1661 µM). The study revealed that the inhibitory effect of flavonoids varies with the number and position of OH groups and bound sugars. Molecular docking analyses indicated that flavonoids exhibited strong interactions with the NADH binding site of LDHA through hydrophobic interactions and hydrogen bonds. Molecular dynamic simulations tested the stability of the fisetin-LDHA complex over 100 ns and showed fisetin's high binding affinity to LDHA, maintaining strong hydrogen bonds. The binding energy of fisetin with LDHA was -33.928 kcal/mol, indicating its effectiveness as an LDHA inhibitor. Consequently, flavonoids identified as strong inhibitors could be potential cancer treatment sources through LDHA inhibition.

Mycobacterium smegmatis putative Holliday junction resolvases RuvC and RuvX play complementary roles in the processing of branched DNA structures

In eubacteria, Holliday junction (HJ) resolvases (HJRs) are crucial for faithful segregation of newly replicated chromosomes, homologous recombination and repair of stalled/collapsed DNA replication forks. However, compared with the Escherichia coli HJRs, little is known about their orthologs in mycobacterial species. A genome-wide analysis of Mycobacterium smegmatis identified two genes encoding putative HJRs, namely RuvC (MsRuvC) and RuvX (MsRuvX); but whether they play redundant, overlapping, or distinct roles remains unknown. Here, we reveal that MsRuvC exists as a homodimer while MsRuvX as a monomer in solution, and both showed high-binding affinity for branched DNAs compared with unbranched DNA species. Interestingly, the DNA cleavage specificities of MsRuvC and MsRuvX were found to be mutually exclusive: the former efficiently promotes HJ resolution, in a manner analogous to the E. coli RuvC, but does not cleave other branched DNA species; whereas the latter is a versatile DNase capable of cleaving a variety of branched DNA structures, including 3' and 5' flap DNA, splayed-arm DNA and double-stranded DNA with 3' and 5' overhangs but lacks the HJ resolution activity. Point mutations in the RNase H-like domains of MsRuvC and MsRuvX pinpointed critical residues required for their DNA cleavage activities, and also demonstrated uncoupling between DNA-binding and DNA cleavage activities. Unexpectedly, we found robust evidence that MsRuvX possesses a double-strand/single-strand junction-specific endonuclease and single-stranded DNA exonucleolytic activities. Combined, our findings highlight that the RuvC and RuvX DNases play distinct complementary, and not redundant, roles in the processing of branched DNA structures in M. smegmatis.

Exploring the Lower Limit of Target Concentration in Capture-SELEX Using Guanine as a Model Target.

During an aptamer selection, using a lower target concentration may result in aptamers with a higher binding affinity. Consequently, this begs the question of whether there is a lower limit for target concentration. In this work, we conducted three aptamer selections using 5 µM, 500 nM and 50 nM guanine as the targets, respectively. Successful enrichment of the same guanine aptamers was achieved at both 5 µM and 500 nM guanine, but not with 50 nM. Using 5 µM guanine, the aptamer was enriched in eight rounds of selection, compared to that for 500 nM, which was accomplished in 17 rounds. We discuss the relation of optimal target concentration to the observed Kd value of the resulting aptamers, of which the highest affinity aptamer had a measured Kd of 200 nM. Additionally, we investigated the binding of the aptamers through mutation studies, revealing a critical cytosine. Mutating this cytosine to a thymine switched the selectivity from guanine to adenine, which is reminiscent of the guanine riboswitch. This study revealed a limit in using low target concentration, and the insights described in this article will be useful for guiding the choice of target concentration during capture-SELEX.

Hepato-renal protective impact of nanocapsulated Petroselinum crispum and Anethum graveolens essential oils added in fermented milk against some food additives via antioxidant and anti-inflammatory effects: In silico and in vivo studies

The study assessed the efficacy of parsley and dill essential oils (EOs) nanocapsules incorporated into fermented milk in hepato-renal protection against specific food additives. A molecular docking assay was conducted between parsley and dill EOs bioactive molecules and inflammatory cytokines. Freeze-dried parsley and dill EOs nanocapsules were developed, characterized for their morphological structure, particle size, zeta potential, polydispersity index and encapsulation efficiency and assessed in fast green dye and sodium benzoate (SB) combination-treated rats. The docking results revealed that the primary constituents of parsley and dill EOs (apiol, myristicin, α-pinene, (−)-carvone, and d-limonene) interacted with the active sites of TNF-α, IL-1β and TGF-1β cytokines with hydrophobic and hydrogen bond interactions. D-limonene had the highest binding affinity (6.4 kcal/mol) for the TNF-α. Apiol and myristicin had the highest binding affinity (5.1, 5.0, 5.0 and 5.0 kcal/mol, respectively) for the IL-1β and TGF-β1 receptors. Biochemically and histopathologically, the excessive co-administration of fast green and SB revealed adverse effects on the liver and the kidney. Whereas the treatment with parsley and dill EOs nanocapsules afford hepato-renal protective effects as manifested by suppression the elevated liver and kidney functions. Parsley and dill EOs nanocapsules showed a significant reduction of the liver (64.08 and 80.5 pg/g, respectively) and kidney (59.3 and 83.6 pg/g, respectively) ROS. Moreover, parsley and dill EOs nanocapsules down-regulated the liver and the kidney inflammatory cytokines (IL-6, TNF-α, IL-1β and TGF-1β) and lipid peroxidation and up-regulated the antioxidant enzymes. In conclusion, the data suggest a potential hepato-renal protective effects of parsley and dill EOs nanocapsules.

Multi-modal neuroprotection of Argemone mexicana L. against Alzheimer’s disease: In vitro and in silico study

Argemone mexicana L. is a medicinal plant, but its impact on Alzheimer's disease (AD) is right now undetermined. We intended to investigate the in-vitro anti-AD potential of leaves and flowers of A. mexicana methanol, ethanol, and ethyl extracts and to identify multi-modal anti-AD phytochemicals by computational approaches. Molecular docking of 196 phytochemicals identified three hit phytochemicals (protoberberine, protopine, and codeine) with higher binding affinity and multi-targeting ability toward AChE, BChE, BACE-1, and GSK-3β. Further MM-GBSA assays confirmed the integrity of these phytochemicals as the hit phytochemicals. However, these phytochemicals demonstrated favorable pharmacokinetics (PK) and drugable properties having no toxicity. Molecular dynamics simulations confirmed the binding strength of the hit phytoconstituents in the active pockets of AChE, BChE, BACE-1, and GSK-3β with multi-targeting inhibitory activities. All the extracts exhibited dose-dependent antioxidant and anti-cholinesterase activities supporting the insilico results in the context of oxidative stress and cholinergic pathways. Our results offer scientific validation of the anti-AD properties of Argemone mexicana L. and identified protoberberine, protopine, and codeine that could be used for the development of multi-modal inhibitors of AChE, BChE, BACE-1, and GSK-3β to combat AD. Additional in vivo validation is recommended to ensure a thorough assessment in the present research.

Nutritional value of a novel EMS-induced cell wall-defective strain of Saccharomyces cerevisiae yeast for Pacific oyster (Magallana gigas) juveniles

The difficulties and high costs of live microalgae production have driven the search for alternative diets in bivalve aquaculture. The baker's yeast (Saccharomyces cerevisiae) represents a promising, cost-effective, high-quality protein for aquaculture. However, its application is restricted by poor digestibility due to its thick, rigid cell wall. Previously, we observed that the deletion of mnn9 gene in S. cerevisiae, leading to defective mannan synthesis and increased β-glucan exposure, enhances growth and immune response in Magallana gigas oysters. Nevertheless, using ∆mnn9 in aquaculture is not feasible due to restrictions on genetically modified organisms (GMO) containing antibiotic-resistance genes. This study aimed to create a non-GMO cell-wall defective yeast mutant (JH40) via ethyl methanesulfonate (EMS) mutagenesis and evaluate its nutritional value for M. gigas juveniles. Phenotypical differences between wild-type S. cerevisiae (WT), ∆mnn9, and JH40 were characterized using fluorescein isothiocyanate (FITC)-labeled lectin analysis, microscopy, cell diameter measurements, growth curves, and osmosensitivity tests. The nutritional value of a microalgae-based diet (Chaetoceros muelleri:Tisochrysis lutea, 50:50 based on dry weight) and its 50% substitution with JH40 or WT was assessed over 21 days in M. gigas juveniles. A complementary test also explored higher substitution levels (63%, 75%, and 100%) of the based diet with JH40 and the addition of extra JH40 (+25 %) in the 63% and 75% replacement diets. Results indicated that JH40 forms clumps, grows slower than the WT, has a larger cell diameter, higher binding affinity to WGA and LEL lectins than the WT, and is highly sensitive to hypo-osmotic stress, which are characteristics of cell-wall defective yeasts. Oysters fed a diet with 50% JH40 substitution showed significantly higher growth compared to those fed the WT-containing diet. JH40 could replace 50% of the algal diet without significantly affecting oyster growth and survival. However, higher inclusion levels of JH40 (62 %, 75 %, and 100 %) did not achieve the oyster growth observed with the algae-based diet, even with additional yeast. These findings are attributed to the limited polyunsaturated fatty acid content in yeast cells. Further research on dosing and administration frequencies is needed to evaluate the immunostimulatory potential of JH40.

In-silico identification of 3,4-Diarylpyrazoles-based small molecules as potential Hsp90 inhibitors

The ATP-dependent molecular chaperone, Hsp90, is crucial for the activity of hundreds of client proteins. Several of Hsp90 clients are involved in cancer cell growth and proliferation. Thus, numerous Hsp90 inhibitors have been developed to target Hsp90′s ATPase activity in cancer cells. CCT018159 is a pyrazole-based compound that successfully inhibited Hsp90 oncogenic activity by binding deeply to the ATP binding pocket in the Hsp90 N-terminal domain (N-Hsp90). In the present study, we utilized the CCT018159 structure to identify new potential Hsp90 inhibitors using a set of in-silico approaches. The ZINC database was virtually screened for CCT018159 analogs using the SwissSimilarity webpage. Ten molecules were selected for further investigation based on their drug-likeness, pharmacokinetics, and physiochemical properties. The molecular docking simulation analysis revealed that these ZINC compounds have Ligand Binding Energies (LBEs) ranging from −8.61 to −9.73 Kcal/mol, which reflects a high binding affinity compared to CCT018159 (LBE of −6.31 Kcal/mol). These compounds exhibited diverse interactions, including critical hydrogen bonds and hydrophobic contacts with crucial residues like Asn51, Ala55, and Leu107. Further optimization targeting unique interactions (e.g., ZINC000008973382 with Asp93, Met98, and Thr184) and exploiting the versatile Lys58 could lead to novel, potent anticancer agents targeting Hsp90.

Cheminformatics-based analysis identified (Z)-2-(2,5-dimethoxy benzylidene)-6-(2-(4-methoxyphenyl)-2-oxoethoxy) benzofuran-3(2H)-one as an inhibitor of Marburg replication by interacting with NP

The highly pathogenic Marburg virus (MARV) is a member of the Filoviridae family, a non-segmented negative-strand RNA virus. This article represents the computer-aided drug design (CADD) approach for identifying drug-like compounds that prevent the MARV virus disease by inhibiting nucleoprotein, which is responsible for their replication. This study used a wide range of in silico drug design techniques to identify potential drugs. Out of 368 natural compounds, 202 compounds passed ADMET, and molecular docking identified the top two molecules (CID: 1804018 and 5280520) with a high binding affinity of −6.77 and −6.672 kcal/mol, respectively. Both compounds showed interactions with the common amino acid residues SER_216, ARG_215, TYR_135, CYS_195, and ILE_108, which indicates that lead compounds and control ligands interact in the common active site/catalytic site of the protein. The negative binding free energies of CID: 1804018 and 5280520 were −66.01 and −31.29 kcal/mol, respectively. Two lead compounds were re-evaluated using MD modeling techniques, which confirmed CID: 1804018 as the most stable when complexed with the target protein. PC3 of the (Z)-2-(2,5-dimethoxybenzylidene)-6-(2-(4-methoxyphenyl)-2-oxoethoxy) benzofuran-3(2H)-one (CID: 1804018) was 8.74 %, whereas PC3 of the 2′-Hydroxydaidzein (CID: 5280520) was 11.25 %. In this study, (Z)-2-(2,5-dimethoxybenzylidene)-6-(2-(4-methoxyphenyl)-2-oxoethoxy) benzofuran-3(2H)-one (CID: 1804018) unveiled the significant stability of the proteins' binding site in ADMET, Molecular docking, MM-GBSA and MD simulation analysis studies, which also showed a high negative binding free energy value, confirming as the best drug candidate which is found in Angelica archangelica which may potentially inhibit the replication of MARV nucleoprotein.

Unravelling the genomic landscape reveals the presence of six novel odorant-binding proteins in whitefly Bemisia tabaci Asia II-1

Genome wide analysis identified 14 OBPs in B. tabaci Asia II-1, of which six are new to science. Phylogenetic analysis traced their diversity and evolutionary lineage among Hemipteran insects. Comparative analysis reclassified the OBP gene families among B. tabaci cryptic species: Asia I, II-1, MEAM1, and MED. The 14 OBPs were clustered on four chromosomes of B. tabaci. RT-qPCR showed high expression of OBP3 and 8 across all body tissues and OBP10 in the abdomen. Molecular docking showed that OBP 3 and 10 had high affinity bonding with different candidate ligands, with binding energies ranging from −5.0 to −7.7 kcal/mol. Competitive fluorescence binding assays revealed that β-caryophyllene and limonene had high binding affinities for OBP3 and 10, with their IC50 values ranging from 9.16 to 14 μmol·L-1 and KD values around 7 to 9 μmol·L-1. Behavioural assays revealed that β-caryophyllene and carvacrol were attractants, β-ocimene and limonene were repellents, and γ-terpinene and β-ocimene were oviposition deterrents to B. tabaci. Functional validation by RNAi demonstrated that OBP3 and OBP10 modulated host recognition of B. tabaci. This study expands our understanding of the genomic landscape of OBPs in B. tabaci, offering scope for developing novel pest control strategies.

Target-specific affinity separation of the bioactive compounds from herbal extract using the spin column packed with the immobilized protein microspheres prior to LC-MS analysis

Excellent pretreatments before instrumental analysis are critical for separation and determination of target compounds for discovery of new drugs from herb medicines. We developed a rapid and highly-selective method to separate the bioactive compounds from herbal extract using protein affinity-selection spin column, which was packed with the new sorbent materials from integrating the recombinant β2-adrenoceptor (β2-AR) directly out of cell lysates onto the surface of microspheres. Protein affinity-selection spin column was placed in a centrifugal tube, where after the non-specific binders were released to the filtrate under the operational centrifugation, the specific binders on the spin column were cleaned with a washing solvent for LC-MS analysis. The known agonists of β2-AR were retained/released on protein affinity-selection spin column but not on control column, demonstrating the method with good recovery (79.4∼95.7 %) and high repeatability (RSD < 3.5 %). The adsorption features of three ligands on the spin column were described best by Prism saturation binding model, and the high-affinity binding and the large binding capacity of the spin column make it feasible to trap the trace analytes effectively. It was applied in separating bioactive compounds from Alstoniae Scholaris extract, two of which were identified as picrinine and oleanolic acid in combination with LC-MS and verified as the potential agonists towards β2-AR though molecular docking and cell experiments. Our study demonstrated that, the spin column with the immobilized protein sorbents in the centrifugal filter device represents a promising tool, enabling rapid and target-specific affinity separation of the bioactive compounds from herbal extract.

Ibuprofen‑derived nitric oxide donors with a high affinity to human serum albumin induce cell death in pancreatic cancer cells through a non‑caspase 3/7‑mediated pathway.

Nitric oxide (NO) has been reported to have a cytotoxic effect on various types of cancer. However, the efficient delivery of NO donors to tumors remains challenging. The present study used ibuprofen, which has a high binding affinity to human serum albumin (HSA). A total of two types of nitrated forms of ibuprofen, 4-[(nitrooxy)methyl]benzyl 2-(4-isobutylphenyl)propanoate [nitrated ibuprofen benzyl linker (NIB)] and 2-(nitrooxy)ethyl 2-(4-isobutylphenyl) propanoate [nitrated ibuprofen ethyl linker (NIE)], were synthesized. It was demonstrated that both NIB and NIE bound to the ibuprofen-binding site of HSA. Although NOx release was observed from NIB, but not NIE, intracellular NO release was detected from both NIB and NIE, which indicated that the mechanisms of NO release may be different for NIB and NIE. Both NIB and NIE induced concentration- and time-dependent cell death in human pancreatic cancer cells, whereas this cell death was not observed with ibuprofen, which could suggest that these cell death-inducing effects may be mediated by NO. The non-specific caspase inhibitor, z-VAD-FMK, inhibited cell death induced by NIB and NIE, but activation of caspase 3/7 was not observed. These results suggested that both NIB and NIE induced cell death through a non-caspase 3/7 pathway. The findings of the present study demonstrated that both NIB and NIE, as NO donors that could be retained in blood, may potentially be useful anti-cancer agent candidates in the future.

Comprehensive study of plasma polymerization parameters on thiol-coated LDPE films for effective fibronectin adsorption targeting biomedical applications

In the realm of biomedical applications, biocompatible materials with optimized surface properties are crucial for facilitating cellular interactions. To attain the perfect balance of these properties, surface modification of non-toxic and stable bulk materials is often required. Within this context, this research aimed to improve the physiochemical and cell-responsive properties of a low-density polyethylene film. This was achieved by depositing thiol-rich coatings using a dielectric barrier discharge plasma reactor operating at medium pressures, with 1-propanethiol serving as polymerization precursor. The study systematically investigated the impact of key plasma polymerization parameters, including DBD chamber pressure, treatment time, and the combination of precursor flow rate and discharge power represented by the Yasuda parameter, to identify optimal plasma processing conditions for the formation of thiol-rich coatings. To characterize the coating thickness, hydrophilicity and surface chemical composition, atomic force microscopy, water contact angle measurements, and X-ray photoelectron spectroscopy were employed. The findings indicated that reducing the chamber pressure to 10 kPa led to more hydrophilic and thicker deposits possessing a higher sulphur content. Deposition time (5 to 15 min) also significantly impacted coating thickness and surface chemistry, where long times increased thickness, but also led to a reduced sulphur and increased oxygen content because of more pronounced etching. The optimal deposition time was therefore set at 10 min resulting in the deposition of dense coatings possessing a high number of sulphur-containing functionalities. The Yasuda parameter (W/FM) analysis demonstrated optimal thiol incorporation in combination with high coating stability at an intermediate W/FM value of 72 MJ/kg. Following the determination of the optimal plasma polymerization parameters, the effectiveness of thiol plasma polymerization and subsequent fibronectin immobilization for enhancing cell adhesion and proliferation was investigated. The thiol-coated substrates were found to exhibit superior protein immobilization, because of the high affinity for protein binding of the available thiol groups. To assess cellular responses, Schwann cells were cultured on uncoated and coated samples before and after fibronectin immobilization. The results revealed a superior cellular response of the thiol-coated samples after fibronectin immobilization, showing the highest cell viability and significantly enhanced cell adhesion and proliferation. Collectively, these results underscore the synergistic effect of thiol plasma polymerization and fibronectin immobilization in promoting the cellular response of LDPE substrates, thus highlighting their potential as a surface modification strategy of biomaterials.

Deciphering Mutational Impacts on c-Src-HK2 Interaction in Colorectal Cancer Progression, and Identification of Potential Phytocompounds Inhibitors: A Molecular Simulation and Free Energy Calculation Approach.

Colorectal cancer (CRC) stands as the third most widespread cancer worldwide in both men and women, witnessing a concerning rise, especially in younger demographics. Abnormal activation of the Non-Receptor Tyrosine Kinase c-Src has been linked to the advancement of several human cancers, including colorectal, breast, lung, and pancreatic ones. The interaction between c-Src and Hexokinase 2 (HK2) triggers enzyme phosphorylation, significantly boosting glycolysis, and ultimately contributing to the development of CRC. The objectives of this study are to examine the influence of newly identified mutations on the interaction between c-Src and the HK2 enzyme and to discover potent phytocompounds capable of disrupting this interaction. In this study, we utilized molecular docking to check the effect of the identified mutation on the binding of c-Src with HK2. Virtual drug screening, MD simulation, and binding free energy were employed to identify potent drugs against the binding interface of c-Src and HK2. Among these mutations, six (W151C, L272P, A296S, A330D, R391H, and P434A) were observed to significantly disrupt the stability of the c-Src structure. Additionally, through molecular docking analysis, we demonstrated that the mutant forms of c-Src exhibited high binding affinities with HK2. The wildtype showed a docking score of -271.80 kcal/mol, while the mutants displayed scores of -280.77 kcal/mol, -369.01 kcal/mol, -324.41 kcal/mol, -362.18 kcal/mol, 266.77 kcal/mol, and -243.28 kcal/mol for W151C, L272P, A296S, A330D, R391H, and P434A respectively. Furthermore, we identified five lead phytocompounds showing strong potential to impede the binding of c-Src with HK2 enzyme, essential for colon cancer progression. These compounds exhibit robust bonding with c-Src with docking scores of -7.37 kcal/mol, -7.26 kcal/mol, -6.88 kcal/mol, -6.81 kcal/mol, and -6.73 kcal/mol. Moreover, these compounds demonstrate dynamic stability, structural compactness, and the lowest residual fluctuation during MD simulation. The binding free energies for the top five hits (-42.44±0.28 kcal/mol, -28.31±0.25 kcal/mol, -34.95±0.44 kcal/mol, -38.92±0.25 kcal/mol, and -30.34±0.27 kcal/mol), further affirm the strong interaction of these drugs with c-Src which might impede the cascade of events that drive the progression of colon cancer. Our findings serve as a promising foundation, paving the way for future discoveries in the fight against colorectal cancer.

BMS345541 is predicted as a repurposed drug for the treatment of TMZ-resistant Glioblastoma using target gene expression and virtual drug screening

Glioblastoma (GBM) is one of the most aggressive and fatal cancers, for which Temozolomide (TMZ) chemo drug is commonly used for its treatment. However, patients gradually develop resistance to this drug, leading to tumor relapse. In our previous study, we have identified lncRNAs that regulate chemoresistance through the competing endogenous RNA (ceRNA) mechanism. In this study, we tried to find FDA-approved drugs against the target proteins of these ceRNA networks through drug repurposing using differential gene expression profiles, which could be used to nullify the effect of lncRNAs and promote the sensitivity of TMZ in GBM. We performed molecular docking and simulation studies of predicted repurposed drugs and their targets. Among the predicted repurposed drugs, we found BMS345541 has a higher binding affinity towards its target protein - FOXG1, making it a more stable complex with FOXG1-DNA. The ADMET analysis of this drug BMS345541 shows a higher half-life and lower cytotoxicity level than other predicted repurposed drugs. Hence, we conjecture that this could be a better drug for increasing the sensitivity of TMZ for treating GBM patients.