Search Results (422)

Cardenolides are an important group of steroidal natural products and have been used successfully for the treatment of cardiovascular diseases by targeting Na⁺/K⁺-ATPase (NKA) and found more recently to show potential anticancer activity. Biological investigations indicate that both the C-17 lactone unit and the C-3 saccharide moiety of these compounds play an important role in their interaction with NKA and in manifesting the resultant bioactivities. Interestingly, the crystal structures of several cardenolides show various conformations, due to a rotation of the C-3 saccharide moiety or the C-17 lactone unit. These rotation conformations could affect their binding to NKA and the resultant bioactivities, and thus docking profiles with NKA for several cardenolides, including cryptanoside A, digoxin and its aglycone, digoxigenin, and gitoxin, have been investigated in the present investigation. The results indicate that the binding poses of the rotation conformations of the cardenolides selected are different when they bind to NKA, as indicated by their docking scores calculated. For each compound, the rotation conformations observed could be in a dynamic equilibrium, of which each conformer may interact with NKA differentially, and these rotation conformers could act on NKA cooperatively to lead to a specific bioactivity. Full article

The aim of this study was to investigate the molecular interactions of heparin, diclofenac, and their supramolecular complexes with cyclooxygenase enzymes (COX-1 and COX-2) using computational docking techniques. Diclofenac is a widely used nonsteroidal anti-inflammatory drug (NSAID) that inhibits COX isoforms, whereas heparin is a polyanionic glycosaminoglycan with established anticoagulant and emerging anti-inflammatory properties. Supramolecular association between these agents may modulate their physicochemical behavior and target engagement. Molecular modeling, dual-drug docking, and molecular dynamics (MD) simulations were employed to characterize the interactions of heparin, diclofenac, and pre-formed heparin–diclofenac complexes with COX-1 and COX-2. Geometry optimization and lipophilicity (logP) estimates were obtained using HyperChem, while protein–ligand docking was performed in HEX using crystallographic COX structures from the Protein Data Bank. Docking poses were analyzed in Chimera, and selected complexes were refined through short MD simulations. Pre-formed heparin–diclofenac assemblies exhibited markedly enhanced docking scores toward both COX isoforms compared with single ligands. Binding orientation strongly influenced affinity: for COX-1, the heparin–diclofenac configuration yielded the most favorable interaction, whereas for COX-2 the diclofenac–heparin configuration was preferred. Both assemblies adopted binding modes distinct from free diclofenac, suggesting cooperative electrostatic and hydrophobic contacts at the enzyme surface. Supramolecular complexation also altered calculated logP values relative to the individual compounds. MD simulations supported the relative stability of the top-ranked complex–COX assemblies. These findings indicate that heparin–diclofenac assemblies may enhance and reorganize predicted COX interactions in a configuration-dependent manner and illustrate the utility of dual-drug docking for modeling potential synergistic effects. Such insights may inform the design of localized or topical formulations, potentially incorporating non-anticoagulant heparin derivatives, to achieve effective COX inhibition with reduced systemic exposure. However, the results rely on simplified heparin fragments, legacy docking tools, and short MD simulations, and should therefore be interpreted qualitatively. Experimental studies will be essential to confirm whether such supramolecular assemblies form under physiological conditions and whether they influence COX inhibition in vivo. Full article

Protein–ligand complexes in crystal structures are well described by an array of bonding interactions among precisely defined functional groups. The present work examines how one representative complex behaves in one-microsecond molecular dynamics simulations, starting from a crystal structure with a native biological ligand bound, and proceeding to simulations of structures derived by docking of that native ligand, and then to docking of selected ligand analogs. The MD behaviors and system energies calculated in RMSD plateau regions using MM/GBSA are similar when initiated from the crystal structure or the structure with the docked native ligand, although independent replicate simulations differ. Despite these similarities, interatomic contact frequencies indicate that some contacts observed in the crystal structure are rarely sampled again; others are sampled only intermittently; and new contacts are recruited that can be more persistent. Docked structures of non-native ligand analogs were chosen for simulation by screening manually for features consistent with known binding interactions, and these displayed behaviors similar to those for the native ligand and, in some cases, similar calculated energies. Overall, ligands appear to cooperate dynamically with the protein in forming the observed interactions. Full article

Antibiotic resistance is an increasing concern in modern healthcare. Therefore, it is important to identify novel antimicrobial agents and new molecular targets for such compounds. Here, we describe the identification of an N-pyridylpyrazolone derivative, 4-(2-aminoethyl)-2-(pyridin-2-yl)-1,2-dihydro-3H-pyrazol-3-one dihydrochloride (compound 1), which is effective against Gram-positive and Gram-negative bacteria and inhibits the enzymatic activity of Escherichia coli L-threonine dehydrogenase (TDH). To characterize its interaction with compound 1, TDH was overexpressed in E. coli. The recombinant enzyme was shown to exist in dilute solution in equilibrium between dimeric and tetrameric forms, with a K_d value for the dimer/tetramer transition of 3 ± 1 nM, and to bind L-threonine cooperatively with a Hill coefficient of 1.4. Compound 1 acted as a partial mixed inhibitor of TDH with an EC₅₀ value of 47 ± 16 µM and did not affect the equilibrium between oligomeric states. Altogether, these findings identify compound 1 as a promising starting point for the development of novel antibiotics and as a tool compound for studying the functional properties of TDH. Full article

Balancing efficiency and equity within agricultural supply chains is crucial for rural revitalization and sustainable development. This study focuses on the three-tiered chain of ‘farmers–cooperatives–retailers’, constructing a joint decision-making model linking pricing, sales effort, and order volume. It compares the performance differences between decentralized and centralized decision-making structures. Methodologically, we introduce four corrective factors—risk-bearing capacity, cooperation level, capital investment, and information access—to the traditional Shapley value. By employing TOPSIS (Technique for Order of Preference by Similarity to Ideal Solution) to calculate proximity, we derive an enhanced Shapley–TOPSIS allocation coefficient. Furthermore, we design a secondary distribution rule of ‘effort-based value-added distribution according to labor contribution,’ tightly binding the marginal returns of sales effort to input intensity, thereby reconciling structural fairness with incentive compatibility. Empirical findings indicate that, compared with decentralized approaches, centralized decision-making significantly enhances overall system revenue and reduces retail prices. The refined distribution scheme outperforms the baseline Shapley value in fairness and stability, effectively mitigating the misalignment where effort contributors receive disproportionately low returns. The optimal sales effort level is approximately 0.35. Under the ‘distribution according to labor’ approach, retailers (the primary effort providers) see a marked increase in their value-added share, whereas farmers and cooperatives also gain positive benefits, enhancing alliance stability. Unlike existing studies that rely mainly on revenue-sharing contracts or a single Shapley allocation, this study, on the one hand, explicitly endogenizes sales effort into demand and profit functions and systematically characterizes the joint mechanism between effort and profit allocation under both centralized and decentralized structures. On the other hand, an improved Shapley–TOPSIS modeling procedure and an ‘effort added-value allocation according to contribution’ rule are proposed. By adjusting demand parameters and the weights of the adjustment factors, the proposed framework can be readily extended to other agricultural products and green supply chain settings, providing a replicable tool and managerial implications for designing sustainable profit allocation schemes. Full article

SH3 domains are widespread protein modules that mostly bind to proline-rich short linear motifs (SLiMs). Most known SH3 domain-motif interactions and canonical or non-canonical recognition specificities are described for individual SH3 domains. Although cooperation and coordinated motif binding between tandem SH3 domains has already been described for members of the p47^phox-related protein family, individual cases have never been collected and analyzed collectively, which precluded the definition of the binding preferences and targeted discovery of further instances. Here, we apply an integrative approach that includes data collection, curation, bioinformatics analyses and state-of-the-art structure prediction methods to fill these gaps. A search of the human proteome with the sequence signatures of SH3 tandemization and follow-up structure analyses suggest that SH3 tandemization could be specific for this family. We define the optimal binding preference of tandemly arranged SH3 domains as [PAVIL]PPR[PR][^DE][^DE] and propose potential new instances of this SLiM among the family members and their binding partners. Structure predictions suggest the possibility of a novel, reverse binding mode for certain motif instances. In all, our comprehensive analysis of this unique SH3 binding mode enabled the identification of novel, interesting tandem SH3-binding motif candidates with potential therapeutic relevance. Full article

The nuclear membrane has emerged as a dynamic regulatory platform coordinating genome organization, mechanotransduction, and regulated cell death (RCD). Beyond its barrier function, the nuclear skeleton—comprising lamins, actin–myosin isoforms, nuclear matrix proteins, and the LINC complex—supports nuclear integrity and gene regulation. Recent evidence shows that type II membrane-bound bZIP transcription factors such as cAMP-responsive element-binding protein 3 (CREB3) and CREB3L1 localize to the inner nuclear membrane (INM), linking chromatin tethering with stress signaling. Their stress-induced cleavage by S1P/S2P disrupts chromatin anchoring and, in some contexts, triggers karyoptosis, a novel form of RCD defined by nuclear rupture. These findings position the nuclear envelope (NE) as a mechanosensitive signaling hub with direct implications for disease and therapy. In this review, we provide a comprehensive discussion on how type II membrane-bound bZIP transcription factors and chromatin acting as a nucleoskeleton cooperate to regulate nuclear membrane integrity. Full article

Background/Objectives: Breast cancer is the most prevalent malignancy among women, and paclitaxel (PTX) is a first-line chemotherapeutic, but chemoresistance driven by ATP-binding cassette (ABC) transporters limits its efficacy. Single-target ABC inhibitors fail due to toxicity and cooperative transporter activity, creating an urgent need for safe multi-target strategies. Membrane cholesterol-rich lipid rafts support ABC transporter function, making cholesterol a key chemoresistance target. This study explored a cholesterol-targeted approach for overcoming PTX resistance. Methods: A PTX-resistant breast cancer line (MCF-7/PTX) showing ABCB1/ABCC3 co-upregulation and enriched cholesterol rafts was established. The effects of Polyphyllin H (PPH), a steroidal saponin from Paris polyphylla, were compared with lovastatin, a biosynthetic cholesterol inhibitor. In vitro and in vivo assays investigated Polyphyllin H’s cholesterol binding and effects on transporters, PTX accumulation, and tumor growth. Results: PPH directly binds membrane cholesterol, disrupting lipid rafts, downregulating ABCB1/ABCC3, reducing drug efflux, and increasing intracellular PTX to restore sensitivity. PPH showed superior cholesterol-binding and resistance-reversal efficacy than lovastatin, with faster, stronger PTX-enhanced cytotoxicity and tumor suppression. Conclusions: PPH reverses PTX resistance by targeting cholesterol-lipid rafts to inhibit multiple ABC transporters. This offers a safer adjuvant for PTX-based breast cancer therapy and a translational framework for other drug-resistant malignancies. Full article

We propose a one-shot, non-cooperative mechanism that implements the core in a large class of public goods games. Players simultaneously choose conditional commitment functions, which are binding unilateral commitments that condition a player’s contribution on the contributions of others. We prove that the set of strong Nash equilibrium outcomes of this mechanism coincides exactly with the core of the underlying cooperative game. We further show that these core outcomes can be found via simple individual learning dynamics. Full article

South Asia’s worsening air pollution crisis represents one of the most urgent public health and environmental challenges of the 21st century. Nearly two billion people—over one-quarter of the global population—reside in this region, where air quality levels routinely exceed World Health Organization (WHO) guidelines by factors of 10 to 15. This has translated into an unprecedented health burden, with approximately two million premature deaths annually, widespread chronic respiratory and cardiovascular disease, and rising economic losses. According to recent World Bank estimates, welfare losses amount to over 5% of regional GDP, a figure far exceeding the projected costs of coordinated mitigation. Despite this, South Asia continues to lack a binding regional framework capable of addressing its shared airshed. Existing cooperative efforts—such as the Malé Declaration on Control and Prevention of Air Pollution (1998)—have provided a useful platform for dialog and pilot monitoring, but they remain voluntary, under-resourced, and insufficient to manage the transboundary nature of the crisis. National-level programs, including India’s National Clean Air Programme (NCAP), Bangladesh’s National Air Quality Management Plan (NAQMP), and Nepal’s National Air Quality Management Action Plan (AQMAP), demonstrate domestic commitment but are constrained by fragmentation, limited financing, and lack of regional integration. This gap represents the central knowledge and governance challenge that prompted the present commentary. To address it, we propose a dual-track architecture designed to institutionalize binding regional cooperation. Track A would establish a United Nations-anchored South Asian Transboundary Air Pollution Protocol, under the auspices of the United Nations Environment Programme, the World Health Organization (WHO), and the United Nations Economic and Social Commission for Asia and the Pacific (UNESCAP). This protocol would codify legally enforceable emission standards, compliance committees, financial mechanisms, and harmonized monitoring. Track B would establish a South Asian Association for Regional Cooperation (SAARC) Prime Ministers’ Council on Air Quality (SPMCAQ) to provide political leadership, align domestic implementation, and authorize rapid responses to cross-border haze events. Lessons from the Indian Ocean Experiment, the ASEAN Agreement on Transboundary Haze Pollution, and Europe’s Convention on Long-Range Transboundary Air Pollution demonstrate that legally binding agreements combined with high-level political ownership can achieve durable reductions in pollution despite geopolitical tensions. By situating South Asia within these global precedents, the proposed framework provides a pragmatic, enforceable, and politically resilient pathway to protect health, reduce economic losses, and deliver cleaner air for nearly one-quarter of humanity. Full article

The bulb of Fritillaria species called “Bei Mu” is a well-known traditional Chinese medicine. We have reported some potential off-target effects of “Bei Mu” due to peimine’s blockade of hERG (human Ether-a-go-go-Related Gene) channels. This research investigated the modulatory effects of three major alkaloid analogs of “Bei Mu” and their cooperative effects on hERG channels using manual whole-cell patch-clamp techniques. Results showed that peiminine and sipeimine blocked hERG currents with IC₅₀s of 36.8 ± 2.5 μM and 47.6 ± 9.8 μM, which were close to that of peimine (26.1 ± 3.5 μM). Peiminine-induced blockade increased with increasing depolarizing strengths, durations, and frequencies, which suggested a preferential binding to open or inactivated states. The reduced blockade by the less inactivating S631A mutation supported peiminine‘s inactivation preference. Molecular docking and dynamics simulations confirmed the hERG-blocking activities of the three alkaloids and provided further insight into potential mechanisms. We also discovered antagonistic effects of the three alkaloids at nearly all concentrations tested, which might help reduce potential cardiotoxicities. To our knowledge, this is the first study to investigate combination effects of chemicals from one herb on hERG channels. In conclusion, peiminine and sipeimine can block hERG channels in a way similar to peimine, but antagonistic effects exist among them. Full article

Sophorolipids (SLs) constitute a group of unique biosurfactants in light of their unique properties, among which their physicochemical characteristics and antimicrobial activity stand out. SLs can exist mainly in acidic and lactonic forms, both of which display inhibitory activity. This study explores the interaction of non-acetylated acidic SL with bovine serum albumin (BSA). SL significantly enhances BSA’s thermal stability, increasing its midpoint unfolding temperature from 61.9 °C to approximately 76.0 °C and ΔH from 727 to 1054 kJ mol⁻¹ at high concentrations, indicating cooperative binding. Fourier-Transform Infrared Spectroscopy (FTIR) analysis confirms SL’s protective effect against thermal unfolding, enabling BSA to maintain its helical structure at 70 °C, distinguishing it from other surfactants that cause denaturation. Furthermore, SL fundamentally alters the sequence of thermal unfolding events; β-aggregation precedes helical domain unfolding, suggesting protective binding to BSA’s helical regions. Computational docking reveals high-affinity binding (Kd = 14.5 μM). Uniquely, SL binds between BSA domains IB and IIIA, establishing hydrophobic interactions, salt bridges, and hydrogen bonds, thus stabilizing the protein’s 3D structure. This distinct binding site is attributed to SL’s amphipathic character. This work deepens the understanding of the molecular characteristics of SL–protein interactions and contributes to improving the general knowledge of this outstanding biosurfactant. Full article

Human methyltransferase-like protein 16 (METTL16) installs N⁶-methyladenosine on U6 small nuclear RNA (snRNA) and other RNAs. Multiple X-ray crystal structures of METTL16 have been published; however, we do not yet fully understand the structure–function relationships of specific residues. We designed 38 mutants, including seven cancer-associated mutants, and used electrophoretic mobility shift assays and single-turnover kinetic assays to better understand the functional roles of specific domains and amino acid residues in binding to U6 snRNA, formation of the METTL16•U6 snRNA•S-adenosylmethionine (SAM) complex, and the rate of methylation. While point mutations in the methyltransferase domain mildly weaken the binding of METTL16 to U6 snRNA, the C-terminal vertebrate conserved regions (VCRs), particularly the arginine-rich region (R382 to R388), mediate cooperative binding and contribute more to RNA binding. All METTL16 K-loop mutants displayed tighter SAM binding, suggesting that the K-loop blocks SAM binding. In addition, residues E133 and F227 are critical for stabilizing SAM binding. Mutations in the ₁₈₄NPPF₁₈₇ catalytic core and R282A abolished methyltransferase activity. Two METTL16 somatic cancer-associated mutants (G110C and R241Dfs*2) displayed reduced methylation activity. This mutational analysis expands our understanding of how specific domains and residues contribute to substrate-binding activity and methylation of U6 snRNA catalyzed by METTL16. Full article

The escalating crisis of multidrug resistance, together with the persistence of antibiotic residues in clinical and environmental matrices, demands integrated strategies that couple sensitive detection, efficient decontamination, and controlled delivery. However, current techniques for quantifying avibactam (AVI)—a broad-spectrum β-lactamase inhibitor—such as HPLC-UV lack the sensitivity and specificity required for both therapeutic drug monitoring and environmental surveillance. Encapsulation of AVI within cyclodextrins (CDs) may simultaneously enhance its stability, bioavailability, and detectability, while the high binding affinities of CDs position them as molecular traps capable of scavenging residual AVI. In this study, the inclusion complexation of AVI with various CDs was examined through molecular dynamics (MD) simulations, experimental isothermal titration calorimetry (ITC), and non-covalent interaction (NCI) analysis. Stable 1:1 inclusion complexes were observed between AVI and β-cyclodextrin (β-CD), 2,6-dimethyl-β-cyclodextrin (DM-β-CD), and 2-hydroxypropyl-β-cyclodextrin (HP-β-CD), with standard Gibbs free energies of binding (ΔG°) of –3.64, –3.24, and –3.11 kcal/mol, respectively. In contrast, γ-cyclodextrin (γ-CD) exhibited significantly weaker binding (ΔG° = –2.25 kcal/mol). DFT-based NCI analysis revealed that cooperative interaction topology and cavity complementarity, rather than the sheer number of localized contacts, govern complex stability. Combined computational and experimental data establish β-CD derivatives as effective supramolecular hosts for AVI, despite an entropic penalty in the DM-β-CD/AVI complex. These CD–AVI affinities support the development of improved analytical methodologies and pharmaceutical formulations, and they also open avenues for decontamination strategies based on molecular trapping of AVI. Full article

DprA (also known as Smf) is a conserved RecA mediator originally characterized by its role in natural chromosomal transformation, yet its widespread presence across bacteria hints at broader DNA metabolic functions. Here, we demonstrate that Bacillus subtilis DprA enhances the frequency of Escherichia coli Hfr conjugation in vivo. In vitro, RecA·ATP binds and cooperatively polymerizes in a 50-nucleotide (nt) polydeoxy T (dT)₅₀ ssDNA to form dynamic filaments that SSB inhibits, an effect fully reversed by Bacillus subtilis DprA. Escherichia coli RecA bound to (dT)₂₁ exhibits minimal dATPase activity, but the addition of B. subtilis DprA significantly stimulates RecA dATP hydrolysis. B. subtilis RecA·dATP readily assembles on (dT)₂₀ complexes, and DprA allosterically activates RecA on even shorter (dT)₁₅ substrates. Combining biochemical assays with a fully atomic model of the RecA–DprA–ssDNA complex, we proposed that only one DNA binding site of the DprA dimer engages the ssDNA during RecA loading, owing to steric constraints. This work refines the mechanism of DprA-mediated RecA nucleation and defines the minimal ssDNA footprint required for mediator activity. Full article