Journal of Molecular Recognition最新文献

Bawei Chenxiang Powder (BWCP) is a Tibetan medicine formulation used to treat cardiovascular diseases, has demonstrated clinical efficacy though its material basis remains unclear. In clinical trial, β₁-adrenergic receptor (β₁-AR) has been recognized as a key therapeutic target in cardiovascular disease treatment. So, in this work, we engineered a fusion protein by linking the kinase domain of epidermal growth factor receptor (EGFR) to the C-terminus of β₁-AR, which was subsequently immobilized onto the ibrutinib-modified silica gels. Following column preparation by packing the β₁-AR immobilized silica into a stainless-steel column, the specificity and stability of β₁-AR column were evaluated through the retention behavior analysis of atenolol, esmolol, and metoprolol for characterization. Then, using the β₁-AR column combined with MS/MS, eight BWCP constituents targeting β₁-AR were screened and identified: 6-hydroxy-2-(2-phenylethyl) chromone, taxifolin, myristicin, costunolide, dehydrocostus lactone, gallic acid, 3,4-dihydroxybenzoic acid (DHBA), and catechin. The association constants of above screened compounds with immobilized β₁-AR were (6.75 ± 0.05) × 10⁴, (13.2 ± 0.60) × 10⁴, (3.82 ± 0.18) × 10⁴, (145.13 ± 1.50) × 10⁴, (199.77 ± 0.30) × 10⁴, (13.8 ± 0.04) × 10⁴, (9.30 ± 0.14) × 10⁴, (31.4 ± 0.76) × 10⁴ M⁻¹, respectively. Molecular docking results indicated that the compound-β₁-AR complexes stabilization primarily involves hydrogen bonding, van der Waals interactions, Pi-alkyl, and Pi-Pi stacking. A survey of DrugBank showed that catechin have well defined effects against cardiovascular diseases. DHBA and taxifolin are potential drug leads under experimental. These confirmed the reliability of the screened compounds by the immobilized β₁-AR. To our knowledge, this work establishes the first systematic identification of BWCP's bioactive components targeting β₁-AR, providing a pharmacological foundation for developing novel cardiovascular therapeutics derived from this traditional formulation.

Sac7d is a 7 kDa protein belonging to the class of the small chromosomal proteins from archeon Sulfolobus acidocaldarius. Sac7d was discovered in 1974 in Yellowstone National Parks geysers, and studied extensively since then for its remarkable stability at large pH and temperature ranges. Sac7d binds to the DNA minor groove, thereby protecting the host genome from extreme conditions by increasing the DNA melting temperature. In this study, we analyzed the Sac7d–DNA complex using 1 μs molecular dynamics simulations. The interaction energy of the interface was decomposed using Molecular Mechanics with Generalized Born Surface Area (MM/GBSA) to determine the residues that contributed most significantly to DNA binding. Out of 12 amino acids considered essential for DNA binding, three were newly identified in this study and had not been previously reported. One of these new amino acids, R63, may be involved in a dynamic protein–DNA interaction. The simulations performed also revealed a sliding motion of Sac7d over double-stranded DNA, suggesting a minimal sequence dependence interaction. Our analysis thus provides novel insights into how the Sac7d chaperones allow to protect DNA from degradation in extreme conditions.

This study aimed to develop a simple, rapid and eco-friendly method for the synthesis of silver nanoparticles (SNPs) employing the aqueous leaf extract of the medicinal plant Dioscorea pentaphylla as a natural and cost-effective reducing and stabilising agent. The synthesised Dp-SNPs were comprehensively characterised using UV–visible, FTIR, HR-TEM, AFM, DLS and XPS techniques. Their in vitro anti-biofilm activity was evaluated against both gram-negative V. cholerae and gram-positive S. aureus, demonstrating potent inhibitory effects against both bacterial strains. To elucidate the interaction between Dp-SNPs and human serum albumin (HSA), multi-spectroscopic techniques were employed. UV–visible and fluorescence analysis revealed a strong binding affinity of Dp-SNPs towards HSA. ITC experiment confirmed that the complexation process was spontaneous and primarily driven by hydrophobic forces. Fluorescence lifetime measurements indicated a static quenching mechanism, and CD spectroscopy suggested minimal alteration in the secondary structure of HSA upon conjugation with Dp-SNPs. Furthermore, an increase in the Zeta potential of Dp-SNPs after binding with HSA suggested improved colloidal stability of the protein–nanoparticle complex. These findings highlight the potential of Dp-SNPs as eco-friendly anti-biofilm agents and provide important insights into their interactions with serum proteins for biomedical applications.

Grb7 is a member of the Grb7 protein family, which also includes Grb10 and Grb14. These adaptor proteins function mainly as scaffolds in phosphorylation-dependent signaling pathways. The family is known to interact with receptor tyrosine kinases and other signaling molecules, and their activity is influenced by protein–protein interactions within their conserved five-domain structure. Grb7 has also been linked to cancer progression and is thought to form dimers and undergo intramolecular interactions that may regulate its signaling functions. In this study, we focused on understanding how the SH2 domain of Grb7 interacts with its RA-PH (RAPH) region, which may partially regulate its overall structure and activity. We introduced five single-site mutations (V45A, R46A, R46K, E47D, S48A) into the SH2 domain and studied their effects using biochemical, biophysical, and computational methods. Circular dichroism (CD) spectroscopy showed that all mutants maintained the overall fold of the SH2 domain. However, the introduction of mutations enhanced the thermal instability of SH2 from 59°C to a range of 56°C–47°C. Surface plasmon resonance (SPR) analysis revealed that mutations at R46 resulted in approximately 1.5–6 times weaker binding to the RAPH region. AlphaFold and ClusPro models and matrices scores supported the biophysical experimental findings. Docking and size exclusion experiments confirmed the RA and PH domains form a stable unit. Truncating the distorted poly-proline region of Grb7 improved its model quality. Collectively, the results provide additional insight into the regulatory mechanisms of Grb7 and may aid in the development of Grb7-signaling dependent cancer therapeutics.

This study compared the inhibitory effects and mechanisms of four sesquiterpene lactones derived from Asteraceae plants on α-amylase using enzymatic kinetics, multi-spectral techniques, and molecular docking methods. It was found that compounds A, B, and C inhibited α-amylase activity through a competitive mechanism, while compound D exhibited non-competitive inhibition, with compound B showing the strongest inhibitory activity. Further analysis revealed that the four sesquiterpene lactone compounds interacted with key amino acid residues of α-amylase via hydrogen bonding and hydrophobic interactions, forming stable protein–ligand complexes. Among them, compound B demonstrated the lowest binding energy, indicating the strongest binding affinity to α-amylase. By investigating the inhibitory effects of these sesquiterpene lactones with a common parent structure on α-amylase, the inhibitory mechanisms and potential pharmacophoric groups were elucidated, providing a scientific foundation for the development of antidiabetic functional foods and drugs based on sesquiterpene lactone scaffolds.

4-Ethyl phenyl sulfate (4-EPS), a gut microbiota-derived metabolite, is identified in ailments like chronic kidney disease (CKD) and numerous neurodegenerative conditions like autism spectrum disorders (ASD). This study is a novel attempt to comprehend the interaction of 4-ethyl phenyl sulfate (4-EPS) with human serum albumin (HSA). This interaction was examined using spectroscopic techniques like circular dichroism (CD), Fourier transform infrared (FTIR), UV–vis absorption, fluorescence spectroscopy, and molecular docking studies. The conformation investigation through FTIR and CD confirmed the alteration in the secondary structure of HSA due to the binding of 4-EPS. Fluorescence spectroscopy revealed the formation of a complex between HSA and 4-EPS upon interaction via static quenching. The spontaneity of the binding process was indicated by the negative ΔG value. Absorption spectroscopy demonstrated that in the presence of 4-EPS (2–48 μM), the absorbance of HSA progressively declined as a result of the formation of the 4-EPS–HSA complex. Contact angle measurements showed the involvement of hydrophobic interactions between HSA and 4-EPS. Molecular modeling was performed, followed by optimization using the DFT approach. Molecular docking study revealed moderate binding between the metabolite and HSA. It was further confirmed that hydrophobic interaction and hydrogen bonds were the main forces responsible for stabilizing the 4-EPS–HSA complex.

Acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) are the main therapeutic targets for the treatment of neurodegenerative diseases, predominantly Alzheimer's disease. This work reports the synthesis, acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) inhibitory activities of synthesized hydrazone Schiff base derivatives of benzimidazole. The compounds have been structurally deduced by means of HR-ESI-MS, ¹H-NMR and ¹³C-NMR techniques and finally assessed for their in vitro AChE and BuChE inhibitory activities. All the compounds attributed notable inhibitory potential with IC₅₀ values ranging from 34.7 ± 0.02 to 185.2 ± 2.47 μM for AChE and 40.8 ± 0.32 to 188.8 ± 2.47 μM for BuChE enzymes. The molecular docking and TD-DFT studies attributed that the compound with methoxy groups, specifically compound (7) displays increased electronic properties and strong dual binding to AChE and BuChE enzymes. Molecular dynamics (MD) simulations for the most active compound (7) were performed, which showed that compound (7) exploits the integral flexibility of AChE and BuChE to encourage conformational variations that lock both enzymes into a two-site inhibitory state. These compounds presented orbitals and favorable electrostatic profiles that improve the inhibitory potential. The results authenticate the SAR trends and highlight the significance of methoxy groups in planning potent cholinesterase inhibitors.

The interaction between ascorbic acid (AA) and a silver nanocluster (Ag₃) is investigated through a combined experimental and theoretical approach. Density Functional Theory (DFT) calculations at the B3PW91/6-311++G(d,p) and LanL2DZ levels revealed that adsorption of AA on Ag₃ induces structural reorganization accompanied by charge transfer from Ag₃ to AA. The charge transfer is confirmed by molecular electrostatic potential (MEP), natural population analysis (NPA), Fukui function analysis, and natural bond orbital (NBO) calculations. The reduced band gap of AA–Ag₃ indicates the interaction between AA and Ag₃. Experimental UV–Vis, Fourier-transform infrared (FTIR), and Fourier-transform Raman (FTR) spectra supported the computational findings, revealing changes in electronic and vibrational modes upon adsorption. The first hyperpolarizability (β) of AA–Ag₃ is calculated to be 21 times higher than that of pristine AA. Open-aperture Z-scan measurements validated the predicted nonlinear optical (NLO) response, demonstrating the potential of the AA–Ag₃ molecular system for advanced NLO device applications.