Journal of Biomolecular Structure & Dynamics最新文献

The over expression of P-glycoprotein (P-gp) is a primary mechanism of multidrug resistance (MDR) in cancer, urgently necessitating the development of novel and effective inhibitors. This work presents a new series of halogenated 4H-pyran-coumarin hybrids designed to overcome this resistance. Six novel hybrids (4a-f) were synthesized and characterized using IR, MS, and 1D/2D NMR techniques. Their antitumor potential was evaluated against sensitive (MCF-7, Caco-2) and resistant (MCF-7/ADR) cancer cell lines, alongside two normal lung cell lines (HFL-1, WI-38), using MTT assays. The ability to inhibit P-gp expression was assessed via ELISA, and efflux pump inhibition was tested with a Rhodamine 123 accumulation assay. Molecular docking and dynamics simulations were employed to investigate interactions with the P-gp binding site. Compounds 4a (2-F), 4c (2-Cl), and 4d (3-Cl) emerged as the most potent leads. They exhibited significant cytotoxicity against MCF-7 (IC₅₀ = 8.14-11.86 µM) and Caco-2 (IC₅₀ = 9.04-13.61 µM) cells and, crucially, effectively reversed P-gp-mediated MDR in MCF-7/ADR cells (IC₅₀ = 15.09-22.79 µM), outperforming Doxorubicin (IC₅₀ = 50.9 µM). These compounds also demonstrated selectivity over normal cells. Mechanistic studies revealed they significantly down regulated P-gp expression. Docking studies confirmed strong binding interactions within the P-gp drug-binding pocket, which were stabilized by key residues like Gln721, as further validated by molecular dynamics simulations. We have successfully developed a novel class of 4H-pyran-coumarin hybrids with potent dual antitumor and MDR-reversal activity. The most promising compounds, particularly the 3-chloro derivative 4d, act through down regulation of P-gp expression and represent highly promising leads for further development as therapeutic agents to combat chemotherapy-resistant cancers.

A multi-step structure-based virtual screening (SBVS) campaign was conducted on a 160,000-compound library to identify novel inhibitors targeting an outer surface region of D-amino acid oxidase (DAO), in the absence of known inhibitor binding geometries. The SBVS workflow incorporated druggability-based filtration and employed three docking engines: sievgene, DOCK 6, and AutoDock Vina. After the final screening stage and selection based on consensus among top-ranked compounds, five candidates were evaluated in vitro. Among them, one compound (N-{[(3S,3aS,6aS)-5-benzylhexahydro-2H-furo[2,3-c]pyrrol-3-yl]methyl}pyridine-3-carboximidic acid) exhibited significant inhibitory activity against DAO. To further refine the docking results and identify the most stable binding pose of the compound, we addressed the post-docking challenge using a combination of molecular dynamics (MD) simulations and machine learning-based hierarchical clustering. Poses generated from the three docking engines were classified using four clustering algorithms, and representative poses for each cluster were subjected to MD and binding free energy calculations via the molecular mechanics/generalized Born surface area (MM/GBSA) method. Notably, three poses converged to a common stable state characterized by the lowest binding free energies. The identified inhibitor in this stable state occupied a region spatially distinct from the substrate-binding site, consistent with our design strategy. Furthermore, we evaluated clustering performance based on the consistency between pose classification and calculated binding free energies. Among the tested methods, nearest neighbor and group average clustering exhibited the highest consistency. These findings demonstrate the utility of an integrated virtual screening strategy, including post-docking analysis to refine binding poses, for the robust identification of surface-binding inhibitors.

Transthyretin (TTR) is a homo-tetrameric transport protein that carries thyroxine (T₄) and retinol-binding protein (RBP). Dissociation of native tetramer of TTR (due to mutations or age-related oxidative modifications) into misfolded monomeric subunits leads to the formation of amyloid fibrils which are deposited in the extra-cellular matrix and eventually cause myriad of human diseases including TTR amyloidosis, diabetes, preeclampsia, cognitive impairment, to name a few. Yet, the role of local micro-environmental factors such as pH in the modulation of tetramer stability is not well-understood. In this study, we performed a systematic analysis of the impact of pH on the structure-function paradigm and aggregation propensity of TTR, using a decreasing pH range of 8.0-2.2. The T₄-binding capacity was preserved at physiological pH, showed marked decrease below pH 6.6 and complete functional loss ≤ 3.3. Structural analyses revealed progressive β-sheet destabilization and increased exposure of aromatic residues. High thermodynamic stability was seen at neutral pH while thermal unfolding at low pH with pH 3.3 exhibiting lowest T_m. Aggregation propensity of TTR was found to be lowest at physiological pH while it formed dense amorphous aggregates at pH 4.4 and distinct ThT-positive amyloid fibrils at pH 3.3. The study defines a pH-dependent threshold for TTR destabilization and aggregation, offering mechanistic insights into amyloid initiation and highlighting local pH as a determinant of disease-relevant aggregation pathways.

Amyloid β (Aβ) peptides, particularly the toxic fragment Aβ_25-35, disrupt lipid bilayers by forming ion channels or inserting into the membrane, which is a key factor in the pathogenesis of Alzheimer's disease. In this study, molecular dynamics simulations were employed to investigate the insertion behavior of β-barrel Aβ_25-35 oligomers in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) membrane. The results demonstrate that embedding the oligomer at a deeper position can enhance the stability of the barrel, and deprotonation of the LYS residue can notably influence its mobility within the membrane and interactions with lipids. During insertion, the protein barrel disrupts local lipid distribution and causes regional thinning of the membrane, but does not affect the overall membrane structural stability. These findings provide a deeper understanding of Aβ-induced membrane disruption mechanisms and offer insights into the membrane-associated pathogenic mechanisms of Aβ_25-35 in the context of Alzheimer's disease.

l-Tyrosine (l-Tyr) is not only a proteinogenic amino acid, but is also a high value natural aromatic compound that serves as a precursor for the biosynthesis of valuable biologically active compounds of pharmaceutical and food industries. In organisms that use the arogenate route for l-Tyr synthesis, a prephenate aminotransferase (PAT) is essential. Studies have demonstrated that this activity is not found independently, but is housed by other aminotransferases. The dapC encoding N-succinyldiaminopimelate aminotransferase (S-DAPAT) of Corynebacterium glutamicum has previously been shown to function as a bifunctional PAT-competent enzyme, as it displays both S-DAPAT and PLP-dependent PAT activities, and its deletion leads to l-Tyr bradytrophy. In this context, a comprehensive biochemical, structural, and phylogenetic characterization of DapC_Cg has been carried out to get clues in the acquisition of PAT activity. Similar to many PAT-competent enzymes, the purified enzyme displayed a strong preference for l-glutamate (l-Glu) as the amino donor to a lesser extent, for l-aspartate (l-Asp) as amino group donors. High prephenate concentrations resulted in substrate inhibition of the enzyme. Sequence and structural alignments with enzymes known to possess PAT activity have shown that key residues that may be critical for activity were conserved. Furthermore, phylogenetic analysis, supported by structural and sequence alignments shed light on the evolutionary trajectory of PAT activity. Based on their evolutionary distance and similarity to S-DAPAT of C. glutamicum in the conserved residues for PAT activity, aminotransferases encoded by pat and hisC of C. glutamicum have been suggested to be involved in l-tyrosine biosynthesis in C. glutamicum.HighlightsDapC bifunctionality in C. glutamicum was characterizedKey residues for prephenate aminotransferase activity were proposedEnzymes with potential to exhibit PAT activity in C. glutamicum were proposed.

Studying aqueous amino acids at low temperatures is crucial for gaining insights into protein behavior, their interactions with water, and their potential applications across various fields. Temperature variations can influence amino acid interactions and conformations, thereby affecting protein stability and functionality. In this study, we aim to investigate the thermoacoustic and thermophysical properties of aqueous alanine by measuring acoustic and related parameters over the temperature range of 303.15 to 278.15 K at atmospheric pressure. The study focuses mainly on the molecular interactions between alanine and water molecules below room temperatures. Using the pulse-echo technique, ultrasonic velocity (u) was measured at a fixed frequency of 5 MHz. The measured ultrasonic velocity (u) of an aqueous alanine towards higher concentrations suggests an increased induced intermolecular interaction between alanine-water molecules. The study also concludes the intermolecular interaction between alanine-alanine molecules towards low temperature via isolated hydrated monomers of alanine. Adiabatic compressibility (β), intermolecular free length (L_f), absorption coefficient (α/f²) and relaxation time (τ) and thermodynamical parameters i.e. the free energy of activation (ΔF), entropy of activation (ΔS) and enthalpy of activation (ΔH) of aqueous alanine solution also supported for the dynamics of aqueous alanine in the icy environment. The significant achievement of the study is that there found a formation of water network (higher values of hydration number) or hydration shell around alanine molecules and induced interaction between nearby alanine molecules in the low temperature region.

In recent years, the development of novel therapeutic strategies to inhibit emerging viruses has become a major challenge in pharmaceutical research. This study aimed to design innovative nanostructures to prevent the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein from interacting with host cells. DNA origami and heparin molecules were incorporated into various nanocomplexes, consisting of a U-shaped DNA origami cage, heparins of different lengths (tetrasaccharide, hexasaccharide, decasaccharide), and a spermidine-functionalized linker positioned near the viral RBD. Molecular dynamics (MD) simulations, complemented by steered MD (SMD) simulations, were performed to evaluate stability and quantify the forces required to detach the RBD. The SMD results reveal strong electrostatic and van der Waals interactions that effectively prevent RBD dissociation. Furthermore, MM/GBSA calculations show negative binding free energies (${\text{ΔG}}_{\text{bind}}$ ranging from - 36.9 ± 7.9 kJ/mol for tetrasaccharide to - 170.9 ± 14.0 kJ/mol for decasaccharide), confirming that longer heparin chains enhance binding affinity and complex stability. These findings underscore the computationally promising potential of these nanostructures for inhibiting viral attachment to the ACE2 receptor. The calculated binding affinity and pulling work further confirm the computationally observed affinity of these nanocomplexes for the RBD. While these computational findings indicate high binding affinity and inhibitory potential, further studies are required to evaluate biocompatibility, stability in biological fluids, immunogenicity, and suitable delivery methods for these nanostructures. This study provides a structural modeling framework integrating DNA origami, heparin, and SMD-MM/GBSA analyses, highlighting the potential of these nanostructures for SARS-CoV-2 inhibition and antiviral therapeutic development.

Lung cancer is the leading cause of cancer-related mortality worldwide and arises from a complex interplay of genetic predispositions and environmental exposures. Epidemiological studies have shown that alterations in key DNA repair genes, such as MSH2, can significantly impact an individual's susceptibility to cancer. In the present study, we focused on MSH2 polymorphisms and their potential role in increasing the risk of lung cancer. Our analysis revealed that four out of six polymorphisms showed a strong association with increased risk of lung cancer in individuals carrying heterozygous or mutant genotypes, specifically 118 T > C, 1032 G > A, T > C/-6, and Asn127Ser. Among these, the T > C/-6 polymorphism exhibited the strongest effect, conferring a 13-fold increased risk of lung cancer (Pcorr = 0.0006) in patients with the variant allele. Stratified analysis further indicated subtype-specific associations: in adenocarcinoma (ADCC) patients, the T > C/-6 variant was linked to a 12-fold higher risk (Pcorr = 0.0018), while in squamous cell carcinoma (SQCC) and small-cell lung carcinoma (SCLC) patients, the same polymorphism was associated with a 2-fold (Pcorr = 0.0006) and 16.5-fold increased risk, respectively, particularly in carriers of the combined or mutant genotypes. MDR analysis predicted the best interaction model (MSH2 118 T > C, IVS 1 + 9 G > C, T > C/-6) with a maximum CVC of 10/10 and the least prediction error of 0.355, accompanied by a significant p-value. Furthermore, MD simulations reveal that the Gly322Asp polymorphism in MSH2 induces pronounced structural destabilisation, which may compromise DNA binding and repair efficiency.

The aggregation of the tau protein into pathological assemblies is a pivotal event in Alzheimer's disease and related tauopathies. Understanding how different cofactors influence the Tau aggregation pathway is crucial for elucidating disease mechanisms. This study directly compares the aggregation pathways of human Tau (hTau441, 4 R/1 N) induced by heparin with those induced by aluminum/sodium fluoride (AlF₃/NaF). We employed time-resolved Raman spectroscopy, a technique uniquely suited for label-free, real-time secondary structure analysis of intrinsically disordered proteins in solution, to monitor structural transitions. Our results reveal two distinct trajectories: Heparin drives a classical pathway of progressive β-sheet enrichment, culminating in mature fibrils. In stark contrast, fluoride conditions suppress β-sheet formation and stabilize granular, nonfibrillar oligomers. These findings suggest that the neurotoxicity associated with fluoride may not arise from accelerating fibril formation but from diverting tau into an off-pathway oligomeric state. This work establishes Raman spectroscopy as a powerful tool for mechanistic studies of protein aggregation and identifies fluoride as a modulator of Tau misfolding with significant pathological implications.

To effectively combat and mitigate the adverse effects associated with the use of bio-based pesticides and to understand their stability in various environmental contexts, it is essential to analyze and fully understand the fundamental characteristics and properties of these complex materials. In this research, a detailed study was conducted to investigate the interaction between chlordecone (CD) and human serum albumin (HSA) under neutral pH conditions. The findings showed that increasing the CD concentration resulted in a significant quenching effect on the static fluorescence emitted by HSA, indicating a significant interaction between the pesticide and the protein. According to thermodynamic analysis and molecular docking data, the binding between CD and HSA primarily occurs within Subdomain IIIB of HSA and is influenced by van der Waals forces, as well as the formation of hydrogen bonds, which play a crucial role in stabilizing the complex. Furthermore, our findings revealed that the presence of CD increased the thermal stability of the protein, a phenomenon that can be attributed to the stabilization of the structural integrity of HSA as a direct result of CD binding. The results obtained from FTIR spectroscopy further confirmed these findings by showing that the presence of CD induces changes in the secondary structure of HSA, leading to structural damage. Furthermore, the use of computational techniques provided further validation of the results obtained through various spectroscopic methods. Taken together, the results of this comprehensive study provide significant insight into the potential health risks that CD may pose to human health.