High Affinity Binding Research Articles

ABSTRACT Psoriasis is characterized by increased levels of pro-inflammatory cytokines, including TNF-α, IL-1β, IL-17A, and NF-κB, as well as keratinocyte hyperproliferation and epidermal thickening. Its pathophysiology is significantly influenced by oxidative stress and abnormal activation of redox-sensitive signaling pathways, such as NF-κB and MAPK. The present study examined the potential of Syringaldehyde (SYD) in the imiquimod (IMQ) induced psoriasis model. Psoriasis Area Severity Index (PASI) scores, back skin thickness, and spleen hypertrophy decreased at dose levels of SYD 25, 50, and 100 mg/kg. Furthermore, a significant reduction in PASI scores following SYD administration indicated a marked improvement in the disease severity and lesion morphology. High-affinity binding of SYD to NF-κB (PDB ID: 4KIK; −34.76 kcal/mol) and MAPK (PDB ID: 1A9U; −32.87 kcal/mol) was found by molecular docking, indicating interference with nuclear translocation and phosphorylation processes. The treatment groups 50 mg/kg and 100 mg/kg indicated restoration of normal histological features. The biochemical evaluation showed decrease in NF-κB, IL-1β, TNF-α, and IL-17 on treatment with SYD. Thus, SYD appears to be a potential therapeutic option for psoriasis, but additional research is needed to confirm its efficacy and safety.

Urolithiasis remains a persistent global health challenge with limited therapeutic options and high recurrence rates. The present study investigated the anti-inflammatory and anti-urolithiatic potential of Ficus religiosa seed extracts through a comprehensive experimental and computational framework. In vitro assays demonstrated that the ethyl acetate extract significantly inhibited red blood cell hemolysis (IC50: 346.63 ± 1.303µg/ml) and protein denaturation (IC50: 524.10 ± 1.29µg/ml), highlighting strong anti-inflammatory effects comparable to diclofenac and acetylsalicylic acid. In the semipermeable membrane model, the ethyl acetate extract exhibited dose-dependent calcium oxalate dissolution, achieving 31.61 ± 0.06% to 84.56 ± 0.03% from 100 to 500µg/ml with an IC₅₀ of 179.99 ± 0.34µg/ml, demonstrating efficacy comparable to that of the reference drug Cystone and surpassing it at higher concentrations. Metabolomic profiling by GC-MS and LC-MS identified 151 phytoconstituents, including flavonoids (quercetin 3'-methyl ether, apigenin), phytosterols (4-cholestenone), and fatty acid esters. Multivariate analyses confirmed solvent-specific clustering, with flavonoid-rich extracts showing superior activity. Network pharmacology integrated these findings, revealing 173 overlapping targets between the identified phytoconstituents and urolithiasis and/or inflammation-associated genes. Functional enrichment analysis highlighted the PI3K-AKT, MAPK, NF-κB, and calcium signaling pathways as key modulatory axes. Molecular docking further validated the high binding affinities of flavonoids and phytosterols with central regulatory proteins such as PI3K, AKT1, IKKβ, MMP-9, and CaMKII, supporting their roles in inflammatory suppression and extracellular matrix remodeling. Overall, this study validates the ethnomedicinal use of Ficus religiosa seeds for the treatment of urinary and inflammatory disorders and highlights their bioactive, multitarget therapeutic potential for managing urolithiasis, warranting further preclinical and clinical evaluation.

Zhishe Tongluo capsule ameliorates experimental ischemic brain injury through regulating the CALB2/Ca2+/PKC pathway and glycerophospholipid metabolism.

Puerarin demonstrates therapeutic potential in alleviating chronic postoperative pain (CPSP) through multi-target mechanisms. While previous studies established its ferroptosis-inhibiting and anti-inflammatory properties via lipid peroxidation reduction and iron-mediated apoptosis regulation, its specific efficacy in CPSP remained unexplored. This study integrated network pharmacology with experimental validation using a skin/muscle incision-retraction (SMIR) rat model. Protein-protein interaction network analysis, Gene Ontology annotation, and KEGG pathway enrichment revealed puerarin's dual action pathway: modulating Th17 cell differentiation and regulating the HIF1 signaling axis. Molecular docking confirmed high-affinity binding between puerarin and five core targets: HIF1A, PTGS2, mTOR, RELA, and GSK3β. In vivo validation showed puerarin significantly elevated mechanical pain thresholds in SMIR rats while downregulating mRNA expression of these targets via qPCR. The compound's multimodal mechanism involves coordinated suppression of inflammatory signaling cascades and hypoxia-responsive pathways. These findings establish a robust methodology combining computational prediction with biological validation for herbal compound research.

The 26S proteasome targets many cellular proteins for degradation during homeostasis and quality control. Proteasome-interacting cofactors modulate these functions and aid in substrate degradation. Here we solve high-resolution structures of the redox active cofactor TXNL1 bound to the human 26S proteasome at saturating and substoichiometric concentrations by time-resolved cryo-electron microscopy (cryo-EM). We identify distinct binding modes of TXNL1 that depend on the proteasome conformation and ATPase motor states. Together with biophysical and biochemical experiments, we show that the resting-state proteasome binds TXNL1 with low affinity and in variable positions on top of the Rpn11 deubiquitinase. In contrast, in the actively degrading proteasome, TXNL1 uses additional interactions for high-affinity binding, whereby its C-terminal tail covers the catalytic groove of Rpn11 and coordinates the active-site Zn2+. Furthermore, these cryo-EM structures of the degrading proteasome capture the ATPase hexamer in several spiral-staircase arrangements that indicate temporally asymmetric hydrolysis and conformational changes in bursts during mechanical substrate unfolding and translocation. Remarkably, we catch the proteasome in the act of unfolding the β-barrel mEos3.2 substrate while the ATPase hexamer is in a particular staircase register. Our findings advance current models for protein translocation through hexameric AAA+ motors and reveal how the proteasome uses its distinct conformational states to coordinate cofactor binding and substrate processing.

The chalcone scaffold pyrazole is important in organic and medicinal chemistry. This study presents the design and synthesis of new chalcone-coupled pyrazole derivatives (1a-1o). The new compounds were characterized using FT-IR, 1H-NMR, 13C-NMR, GC-MS, elemental analysis, and cytotoxic analysis on MCF-7 and HepG2 cancer cell lines. The synthesized compounds also underwent molecular docking, ADMET (absorption, distribution, metabolism, excretion, and toxicity), and DFT (density functional theory) studies. Compound 1a showed high cytotoxic activity against MCF-7 cells (LC50, 0.62 ± 0.01 µM), outperforming standard Doxorubicin. Compounds were examined using molecular docking, ADME-T, and DFT calculations. Compound 1a had a higher binding affinity (-10.8 Kcal/mol) than Doxorubicin (-4.7 Kcal/mol). ADME-T profile and pharmacokinetic predictions were performed on the analogs. DFT with the B3LYP/6-311++G (DP) basis set helped determine optimal shape and dimensions. Additional Gaussian 16-based DFT calculations were conducted on compounds (1a-1o). The HOMO-LUMO analysis revealed compound 1a had a significant energy gap (2.5056 eV, from -7.94026 eV to -5.43465 eV). Compound 1a may be a promising anti-cancer agent.

Background/Objectives: Glioblastoma multiforme (GBM) is an aggressive primary brain tumor with limited therapeutic options. Neoantigen-based immunotherapy offers a promising avenue, but its efficacy primarily depends on the ability of somatic mutations to generate immunogenic peptides effectively presented by HLA class I molecules and recognized by cytotoxic T cells, in concert with innate immune mechanisms such as NK-cell activation and DAMP/PAMP signaling. This study aimed to characterize the MHC-I binding diversity of peptides derived from GBM-associated somatic variants, with a particular focus on interactions involving HLA-A68:01 and HLA-B15:01 alleles. These alleles were selected based on their ethnic prevalence and potential structural compatibility with neoepitopes. Methods: Somatic missense variants from TCGA-GBM were filtered using high-confidence genomic databases, including dbSNP, COSMIC, and MANE. Neoepitope prediction was performed across multiple HLA class I alleles using binding affinity algorithms (MHCflurry2). Peptide–HLA interactions were characterized through motif analysis and anchor residue enrichment. Structural modeling of peptide–HLA complexes was conducted using ColabFold (AlphaFold2-multimer v3) to evaluate conformational stability. The population frequency of selected HLA alleles was examined through epidemiological comparisons. Results: Canonical GBM driver mutations (e.g., EGFR, TP53, PIK3R1) are recurrent and biologically relevant, although pharmacological inhibition of EGFR alone has not consistently improved patient outcomes, underscoring the complex signaling redundancy in glioblastoma. HLA-A68:01 exhibited high binding affinity and favorable motif compatibility, supporting its potential for effective neoantigen presentation. HLA-B15:01 was identified as a viable presenter for the EGFR p.Arg108Lys variant. Structural modeling confirmed stable peptide insertion into the MHC-I binding groove, with high-confidence folding and preserved interface integrity. Ethnic distribution analysis revealed varying GBM incidence across populations expressing these alleles. Conclusions: This integrative analysis identified structurally validated, immunogenically promising neoantigens derived from GBM mutations, particularly for HLA-A68:01 and HLA-B15:01. These findings support allele-informed neoepitope prioritization in personalized immunotherapy, especially for patient populations with corresponding HLA genotypes and MHC-I presentation capacity.

Deubiquitinases (DUBs) are pivotal in cancer progression, yet their role in metabolic reprogramming in gastric adenocarcinoma (GAC) remains unclear. Here, we discover that highly expressed PSMD14 strengthens tumor stemness and drives tumor progression by increasing glycolysis and lactate accumulation, which activates H3K27 lactylation (H3K27la) and turns to enhance the expression of PSMD14 and SOX9. Mechanistically, PSMD14 deubiquitinates PFKFB2 at K355, facilitating SCYL2-mediated phosphorylation of PFKFB2 at S466/S483, which increases the generation of fructose-2,6-bisphosphate, activating PFK1 and glycolysis. Additionally, the H3K27la/PSMD14/SCYL2/p-PFKFB2 axis correlates with increased glucose metabolic activity and poor prognosis in GAC patients. Notably, high-throughput screening of FDA-approved drugs reveals that Daclatasvir (DCV) exhibits high binding affinity for PSMD14 protein, disrupts the PSMD14-PFKFB2 interaction, reduces PFKFB2 activity and tumor burden. Collectively, our findings are the first to elucidate a positive feedback loop existing between PSMD14 and glycolysis in GAC progression, suggesting that PSMD14 blockade may represent a potential therapeutic approach for GAC.

Alzheimer's disease is characterized by the aggregation of the Aβ peptide into amyloid fibrils. According to the amyloid hypothesis, pharmacologicallytargeting Aβ aggregation could result in disease-modifying treatments. The identification of inhibitors of Aβ aggregation, however, is complicated by complex technical challenges, which typically restrict to tens of thousands the number of compounds that can be screened in experimental aggregation assays. Here, we report a computational route to increase by 4 orders of magnitude the number of screenable compounds. We achieve this result by developing an open source pipeline version of the Deep Docking protocol, and illustrate its application to the discovery of secondary nucleation inhibitors of Aβ aggregation from an ultra-large chemical library of over 539 million compounds. The pipeline was used to prioritize 35 candidate compounds for in vitro testing in Aβ aggregation assays. We found that 19 of these compounds inhibit Aβ aggregation (54% hit rate). The two most potent compounds showed potency better than adapalene, a previously reported potent inhibitor of Aβ aggregation. Consistent with the intended mechanism of action, these two compounds also proved to be high-affinity binders of Aβ fibrils with an equilibrium dissociation constant in the low nanomolar range in surface plasmon resonance experiments. These results provide evidence that structure-based docking methods based on deep learning represent a cost-effective and rapid strategy to identify potent hits for drug development targeting protein misfolding diseases.

Alzheimer's disease (AD) is a neurodegenerative disorder characterized by dementia and inexorable loss of neurons. Despite extensive research, the currently approved drugs offer only limited efficacy which highlights the need for exploring novel synergistic natural compounds capable of mitigating multiple targets of AD. This study evaluated the neuroprotective potential of the synergistic combination of Vitexin and Thymol using computational and in vitro model systems in N2a cells. Computational pharmacokinetic screening revealed the blood-brain barrier (BBB) permeability of thymol and 0.55 bioavailability score for Vitexin. Molecular docking studies showed higher binding affinity of Vitexin with JNK and Thymol with COX-1 and CAMK-II and 100 ns molecular dynamics simulation exhibited stable binding with sustained hydrogen bond and hydrophobic interactions. Based on the IC50 values [Vitexin (135.24µg/ml, 312.9 µM) and Thymol (36.91µg/ml, 245.7 µM)] and combination index (CI < 1) determined by the acetylcholinesterase (AChE) inhibition assay and checkerboard assay (performed with 15 different combinations) respectively, the effective combination (Vitexin 45.08µg/ml; Thymol 7.382µg/ml; CI = 0.53) was fixed for further studies. In okadaic acid (OA) induced neurotoxicity model, pre-treatment with the combination significantly increased the cell viability (88.36 ± 3.73%) (n = 3). Real-time PCR results revealed the upregulation of PP1 gene expression and modulation of MAPK family (MEK1/2, ERK1/2 and JNK), and other tau related kinases (GSK3β, CAMKII and P70 s6). The above findings demonstrate that the combination of Vitexin and Thymol effectively protect the neuronal cells from OA induced cytotoxicity and modulate the hyperactivation of kinases, suggesting its potential in preventing tau hyperphosphorylation in AD conditions.

ABSTRACT The management of iodine species, notorious for their environmental persistence and health risks, requires innovative materials capable of efficient capture and conversion. Herein, we report the self‐assembly and characterization of a Zr‐based metal–organic tetrahedron ( 1 ) functionalized with redox‐active triazatriangulenium (TATA + ) panels. The cage exhibits a high binding affinity for triiodide (I 3 − ) (ca. 10 6 M −1 ) in methanol. The strong host–guest complexation significantly facilitates the disproportionation hydrolysis of I 2 to generate I 3 − and HOI. It also enables photocatalytic aerobic oxidation of I − into I 3 − within its cavity. Mechanistic investigations revealed the key steps involving guest‐to‐host photoinduced electron transfer (ET) to generate radicals I • and 1 • and ET from 1 • to dioxygen to generate superoxide. Solid‐state adsorption experiments showed the rapid removal of I 2 and I 3 − from water by 1 ‐NTf 2 because of the high affinity for polyiodides. Importantly, although solid‐state 1 ‐NTf 2 has no ability to directly adsorb I − from water, we have for the first time developed a light‐driven strategy that enables removal of I − through coupled photooxidation and sequestration. This work highlights the significant potential of integrating photoredox‐active moieties within stable metal–organic cages for controlling iodine binding and speciation and opens new avenues to address environmental and energy‐related sequestration challenges.

Targeted protein degradation via PROTACs holds promise for antiviral therapy but is challenged by inefficient ternary complex formation. We report the de novo design of PROTACs targeting the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp). Leveraging repurposed antiviral scaffolds and optimizing E3 ligase ligands, we designed and screened 600 candidates. Our integrated pipeline identified PROTAC 10, a molnupiravir-CRBN conjugate, which demonstrated high-affinity binding (Kd = 1.09 nM), pronounced positive cooperativity (α = 45.9), and effective CRBN-mediated RdRp degradation (DC50 = 1.97 μM) in infected cells. PROTAC 10 was synthesized by using modular click chemistry (CuAAC), strategically incorporating a central triazole ring flanked by flexible alkyl spacers. It exhibited potent antiviral activity (IC50 = 3.12 μM). Molecular dynamics simulations revealed that its engineered linker enhances cooperativity, ternary complex stability (ΔGTER = -247 kcal/mol), and chameleonic character. This study provides a strategic framework to design antiviral PROTACs through rational linker optimization that enables selective viral protein degradation.

Kirkia tenuifolia Engl. (family Kirkiaceae) is traditionally used to treat cholera, alleviate thirst, and serves as an important water source and livestock feed in arid regions. However, to date, no scientific study has been conducted on its chemical composition and pharmacological properties. Therefore, the present study aimed to isolate and identify the chemical constituents from the stem bark of Kirkia tenuifolia Engl and evaluate their pharmacological activities. Silica gel chromatographic separation of the methanol extract afforded nine compounds (1–9), identified herein for the first time from this species. Among them, lupeol (2) exhibited notable antibacterial activity with an MIC of 0.625 mg/mL against E. coli, S. typhi, and P. aeruginosa. Dimethylfraxetin (5), urolithin M5 (6) and urolithin M5 (7) showed antibacterial activity with an MIC of 0.625 mg/mL against E. coli and P. aeruginosa. Compounds 2, 5, 6, and 7 demonstrated potent antioxidant activities in the DPPH assay, with IC₅₀ values ranging from 2.58 to 9.00 µg/mL. The methanol extract showed significant cytotoxicity against MCF-7 breast cancer cells (34.96% viability at 200 µg/mL) and antiviral activity against influenza A (H1N1) (CC₅₀ = 39.8, IC₅₀ = 4.2 µg/mL, SI = 9.1). Molecular docking revealed that compound 7 exhibited higher binding affinities with S. aureus pyruvate kinase (-7.2 kcal/mol) and L. monocytogenes receptor (-7.4 kcal/mol) compared to ciprofloxacin (-5.6 and − 6.2 kcal/mol, respectively). Lupeol (2) showed stronger binding to Prdx5 (-6.1 kcal/mol) than ascorbic acid (-5.2), while compounds 2, 5, 6, and 7 bound more strongly to human myeloperoxidase (-7.4 to -8.6) than ascorbic acid (-4.8). These findings support the therapeutic potential of Kirkia tenuifolia Engl, but further studies are needed to confirm its effects against diverse pathogens and cell lines.

Abstract Anionic surfactants are essential additives for leather-making, routinely employed on beamhouse processes in combination with industrial enzyme preparations. However, few studies have elaborated the effects of surfactants on bacterial collagenase—a harmful component in industrial enzyme preparations that degrade collagen and impair leather quality. Here, we investigated the effects of two anionic surfactants, sodium dodecyl sulfate (SDS) and sodium dodecyl benzene sulfonate (SDBS), on the activity of collagenase G (ColG), a representative bacterial collagenase. The results showed that both anionic surfactants could significantly inhibit the hydrolytic activity of ColG. In comparison with SDS, SDBS exhibited a stronger inhibitory effect on ColG at lower concentrations. Spectroscopy, molecular docking, and molecular dynamics simulation were employed to investigate the surfactant-bacterial collagenase interactions. The results indicated that both SDS and SDBS inhibited ColG primarily by occupying the active site of ColG and inducing conformational changes in the catalytic region. Compared with SDS, SDBS exhibited significantly higher binding affinity toward ColG and induced more pronounced conformational alterations of collagenase, resulting from π-conjugation effects and steric hindrance of its benzenesulfonate moiety. These findings not only facilitate optimized coordination between surfactants and industrial enzymes in leather-making processes but also provide theoretical support for developing bacterial collagenase inhibitors. Graphical Abstract

Oleandrin-mediated suppression of MELK induces apoptosis, autophagy, and ferroptosis in human non-small cell lung cancer cells.

The role of mineralization bacteria in the immobilization of cadmium and lead in aqueous solutions.

Amphiphilic cationic 2-morpholinoethanol analogues synthesis and study of N-alkylation role in self-assembly and anticandida activity.

Unveiling the therapeutic potential of artopetelin flavonoids through computational approaches as peroxisome proliferator-activated receptor-delta (PPARδ) agonists.

Novel graph neural network reveals binding mechanisms and environmental risks of PAHs interaction with estrogen receptor B.

Computational design of Fusarium solani cutinase variants for efficient polylactide and polyethylene terephtalate hydrolysis.