Molecular insight into binding behavior of caffeine with lactoferrin: Spectroscopic, molecular docking, and simulation study

Exploring the binding mechanism and functional properties of lactoferrin-berberine complex: Based on multispectral analysis, molecular docking, and dynamics simulations

Denaturation and/or aggregation of proteins under adverse environmental conditions can greatly impair their bioactivity and functional properties. Based on this, this study aims to improve the functional properties of lactoferrin by complexing with berberine and investigate the mechanism using multispectral techniques, molecular docking and dynamics simulations. The results showed that berberine bound to lactoferrin through hydrogen bonding and van der Waals forces and altered its conformation, surface hydrophobicity, amino acid microenvironment, and secondary structure. Molecular docking and dynamics simulations further revealed that berberine inhibited the drastic changes in the lactoferrin structure, contributing to the complex stability. Consequently, the denaturation temperature and degradation temperature (224 °C to 230 °C) and the tolerance to extreme pH, high temperature, and ions of the lactoferrin-berberine complex were improved. This study systematically revealed the mechanism of berberine to improve the functional properties of lactoferrin, contributing to the development and application of novel functional ingredients.

Effect of chitooligosaccharide on the binding domain of the SARS-COV-2 receptor

The receptor-binding domain (RBD) is crucial for understanding how severe acute respiratory syndrome coronavirus (SARS-CoV-2) recognizes and infects host cells. Chitooligosaccharide (CS) exhibits diverse antiviral activities, with its derivatives showing remarkable efficacy in blocking SARS-CoV-2 infection. Thus, this study employed spectroscopy, virus-infected cell experiments, and molecular simulation to investigate the molecular interactions between CS and SARS-CoV-2 RBD, as well as their mechanisms. In spectroscopic experiments, all four CS variants with different molecular weights formed interactions with the RBD. These variants increased the resistance of HEK293ACE2 cells to SARS-CoV-2 invasion. Molecular docking revealed that the four CS variants could bind to the RBD through hydrogen bonding or salt-bridge interactions, forming stable complexes. Chitotetraose provided stronger protection to HEK293ACE2 cells compared to other CS variants and displayed higher molecular docking scores. Further investigation into the optimal docking conformation of chitotetraose was conducted through molecular dynamics simulation methods. This study lays a solid theoretical foundation and provides a scientific basis for the development of targeted RBD inhibitors, as well as drug screening and application against novel coronaviruses.

Exploring the therapeutic potential of rutin through investigating its inhibitory mechanism on lactate dehydrogenase: Multi-spectral methods and computer simulation

Lactate dehydrogenase (LDH), a crucial enzyme in anaerobic glycolysis, plays a pivotal role in the energy metabolism of tumor cells, positioning it as a promising target for tumor treatment. Rutin, a plant-based flavonoid, offers benefits like antioxidant, antiapoptotic, and antineoplastic effects. This study employed diverse experiments to investigate the inhibitory mechanism of rutin on LDH through a binding perspective. The outcomes revealed that rutin underwent spontaneous binding within the coenzyme binding site of LDH, leading to the formation of a stable binary complex driven by hydrophobic forces, with hydrogen bonds also contributing significantly to sustaining the stability of the LDH-rutin complex. The binding constant (Ka) for the LDH-rutin system was 2.692 ± 0.015 × 104 M-1 at 298 K. Furthermore, rutin induced the alterations in the secondary structure conformation of LDH, characterized by a decrease in α-helix and an increase in antiparallel and parallel β-sheet, and β-turn. Rutin augmented the stability of coenzyme binding to LDH, which could potentially hinder the conversion process among coenzymes. Specifically, Arg98 in the active site loop of LDH provided essential binding energy contribution in the binding process. These outcomes might explain the dose-dependent inhibition of the catalytic activity of LDH by rutin. Interestingly, both the food additives ascorbic acid and tetrahydrocurcumin could reduce the binding stability of LDH and rutin. Meanwhile, these food additives did not produce positive synergism or antagonism on the rutin binding to LDH. Overall, this research could offer a unique insight into the therapeutic potential and medicinal worth of rutin.

Inhibition effect of epicatechin gallate on acid phosphatases from rainbow trout (Oncorhynchus mykiss) liver by multispectral and molecular docking

Inhibition of acid phosphatase, which significantly contributes to inosine 5'-monophosphate (IMP) degradation, is crucial for preventing flavor deterioration of aquatic products during storage. In this study, the inhibitory effect of epicatechin gallate (ECG) on the activity of acid phosphatase isozymes (ACPI and ACPII) was analyzed using inhibition kinetics, fluorescence spectroscopy, isothermal titration calorimetry, and molecular simulation. ACPI and ACPII with molecular weights of 59.5 and 37.3 kDa, respectively, were purified from rainbow trout liver. ECG reversibly inhibited ACPI and ACPII activities via mixed-type inhibition, with half maximal inhibitory concentration (IC50) of 0.24 ± 0.01 mmol/L and 0.27 ± 0.03 mmol/L, respectively. Fluorescence spectra indicated that ECG statically quenched the intrinsic fluorescence of ACPI and ACPII. ECG could spontaneously bind to ACPI and ACPII through hydrogen bonding and van der Waals forces and exhibited a higher affinity for ACPI than for ACPII. In addition, molecular dynamic simulation revealed that ECG-ACPI and ECG-ACPII complexes were relatively stable during the entire simulation process. Our findings provide a theoretical basis for the use of ECG as an inhibitor of ACP to improve the flavor of aquatic products.