Molecular simulation for food protein-ligand interactions: A comprehensive review on principles, current applications, and emerging trends

Investigation of self-assembly mechanism of gluten protein amyloid fibrils and molecular characterization of structure units

The mechanism of peptides self-assembly into gluten amyloid fibrils was explored through bond-breaking experiments and molecular dynamics (MD) simulations, verified through fibrillation experiments using synthetic peptides. The disruption of hydrogen bonds reduced thioflavin T fluorescence intensity and average particle size of gluten amyloid fibrils by 24 % and 81 %, respectively, causing a breakdown of internal structure. Disruption of electrostatic and hydrophobic forces induced further aggregation of fibrils. MD simulation revealed that peptides transitioned from a dispersed state to aggregation, followed by changes in secondary structure, culminating in the formation of stacked β-sheets structure units. Hydrogen bonding emerged as the primary driver of self-assembly with contributions from hydrophobic and electrostatic interactions. The synthetic single or hybrid peptide systems selected by MD formed ribbon- or fiber-like amyloid fibrils with inter-strand distance of 4.7 Å and respective inter-sheet distances of 10.2 Å and 10.8 Å, suggesting that the structure and morphology of eventual amyloid fibrils were affected by the peptide sequence and cross β-sheet structure units.

Active induction: a promising strategy for enhancing the bioactivity of lactic acid bacteria

Lactic acid bacteria (LAB), as key probiotic, play crucial roles in maintaining human health. However, their survival and functionality in diverse habitats depend on their ability to sense and respond to environmental stresses. Notably, active induction has emerged as a promising strategy for regulating the biological activity of LAB, potentially enhancing their health benefits. Therefore, this review summarizes the beneficial effects of active induction, including acid, bile, oxidation, ethanol, heat, cold, and radiation induction on the functional activities of LAB. In addition, omics methods, in silico analysis, and gene editing technologies have greatly facilitated the profound exploration of the stress regulatory network in LAB, thereby aiding the identification of active components and stress adaptors. Through these advancements, LAB provide health benefits by regulating stress-related genes and proteins, as well as inducing bioactive metabolite production. As a result, they could enhance stress tolerance, cross-protection, intestinal colonization, adhesion properties, and provide antialcohol and liver protection in vitro or in vivo. This study highlights the potential of active induction strategies in enhancing the functional role of LAB in food applications.

Molecular mechanisms of Lycii Fructus (Goji berries) against xanthine dehydrogenase in hyperuricemia management: Integrating computational, metabolomic, and experimental approaches

Lycii Fructus (LF), commonly known as Goji berries, has shown potential for managing hyperuricemia, though its underlying mechanisms remain poorly understood. This study employs a combination of network-based systems pharmacology, computer-aided drug discovery, untargeted metabolomics and experiments to explore the urate-lowering effects of LF. Molecular docking simulations of 3,760 LF compound-target interactions identified xanthine dehydrogenase (XDH) as a key target. Among the compounds, glycitein exhibited the highest binding affinity in molecular dynamics simulations. Metabolomics confirmed the presence of glycitein in LF particles, and it significantly reduced urate levels in hyperuricemia zebrafish models. Further in vitro assays and Cellular Thermal Shift Assays corroborated its inhibitory effect on xanthine oxidase. These findings suggest that glycitein may serve as a novel inhibitor of xanthine oxidase, with potential applications in nutraceuticals, functional foods, and drug development for hyperuricemia.

Explore the toxicological mechanism of 6PPD-Q on human health through a novel perspective: The interaction between lactate dehydrogenase and 6PPD-Q

N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine-quinone (6PPD-Q), an oxidative derivative of tire anti-degradant, has been linked to mortality in coho salmon (Oncorhynchus kisutch) and has exhibited potential human toxicity. Hence, exploring how 6PPD-Q interacts with biomacromolecules like enzymes is indispensable to assess its human toxicity and elucidate its mechanism of action. This investigation aims to explore the impact of 6PPD-Q on lactate dehydrogenase (LDH) through various methods. The findings indicate that 6PPD-Q can spontaneously embed in the coenzyme site of LDH and obviously change the biological activity of LDH by non-competitive inhibition. Simultaneously, this inhibitory effect is concentration-dependent. 6PPD-Q can affect both the level of LDH and the transcription of Ldha in AML-12 cells. Hydrogen bonding and van der Waals forces serve as the primary driving forces in LDH-6PPD-Q combination process. The apparent binding constant (Ka) value is (9.773 ± 0.699) × 103 L/mol (298 K). The presence of 6PPD-Q alters the conformation of LDH and decreases its structural stability. Moreover, the results of molecular docking indicate that the interaction of 6PPD-Q with Asp51 and Arg98 of LDH may be the reason that 6PPD-Q inhibits the biological activity of LDH. Meanwhile, the energy decomposition of residue analyses for LDH-6PPD-Q formation further highlight the energy contribution of Asp51 and Arg98 in this combination process.

Network pharmacology and molecular analysis of mechanisms underlying the therapeutic effects of Rhubarb in treating atherosclerosis and abdominal aortic aneurysm

Aim of the study

The aim of this study was to systematically investigate the effects and mechanisms of Rhubarb in the treatment of Atherosclerosis (AS) and Abdominal Aortic Aneurysm (AAA) by utilizing network pharmacology and molecular docking techniques.

Materials and methods

TCMSP systematic pharmacology database was utilized to search for active chemical components of Rhubarb. Disease-related targets were retrieved from the GEO dataset and Disgenet database. Gene interactions were utilized to identify common targets of Rhubarb with AS/AAA, and interaction networks were constructed using Cytoscape 3.9.1. Protein-protein interaction (PPI) networks for the core targets were constructed using the STRING database. GO and KEGG pathway enrichment analysis was performed using DAVID. Molecular docking is used to assess the potential target-active compound interactions.

Results

In our study, 16 active compounds were screened from Rhubarb, along with 310 targets. Additionally, 110 AS/AAA target genes were screened out. Topological analysis of the PPI protein network yielded 23 core targets. The targets, biological functions and signaling pathways of Rhubarb in AS/AAA were further investigated. The analysis indicated that Rhubarb may be effective in treating AS/AAA through processes such as lipids, atherosclerosis, extracellular matrix catabolism, collagenolytic metabolic processes, and the extracellular environment. Five core pharmacological targets were also identified: TNF, IL-1β MMP9, TP53, and PPARG. Molecular docking showed a strong binding ability between the active compounds and the screened targets.

Conclusions

This study successfully predicted the molecular functions, pharmacological targets, and pathways associated with Rhubarb for treating AS/AAA. In addition, identified potential active ingredients can be used as a source for AS/AAA drug screening.

De novo in silico screening of natural products for antidiabetic drug discovery: ADMET profiling, molecular docking, and molecular dynamics simulations

Epigenetic dysfunction which has implicated disease conditions such as diabetes highlights the urgency for the discovery of novel therapeutic alternatives. The rising global incidences of diabetes and the limitations of existing treatments further exacerbate the quest for novel antidiabetic agents' discovery. This study leverages computational approaches to screen selected bioactive natural product phytoconstituents for their potential anti-diabetic properties. Utilizing pharmaceutical profiling, ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) predictions, molecular docking, and molecular dynamics (MD) simulations, the drug-likeness and binding affinity of these natural compounds against human pancreatic amylase was investigated. Out of the total 24,316 ZINC compounds screened for their binding scores with amylase, ZINC85593620, ZINC85593668, and ZINC85490447 came top. The compounds had higher binding scores than the standards (acarbose and ranirestat) with ZINC85593620 having the highest docking score of - 12.162 kcal/mol and interacted with key amino acid residues such as TRP 59, ILE 148, and ASP 197. Further validation through MD simulations reveals that all the compounds showed minimal fluctuations relative to the standards indicating strong and stable binding interactions suggesting potential effective inhibition of the enzyme. ZINC85593620 and ZINC85593668 showed promising distribution and availability characteristics for amylase inhibition. Overall, the compounds displayed potential amylase inhibition which underscores their use as promising natural products in developing new antidiabetic drugs. Further experimental validations are recommended to offer a potential solution to the pressing need for safer and more effective antidiabetic therapies.

Screening and evaluation of novel DPP-IV inhibitory peptides in goat milk based on molecular docking and molecular dynamics simulation

Virtual screening techniques have gained much attention as a means of studying bioactive peptides. This study aimed to screen DPP-IV inhibitor peptides in goat milk after simulated digestion in vitro combined with molecular docking and dynamics simulations. By evaluating the docking energy and active sites, and by analyzing RMSD, RMSF, and Rg values, two novel peptides, GPFPLL and LPYPY, were successfully screened and identified. GPFPLL and LPYPY were found to exhibit high inhibitory activity against DPP-IV (IC50 of 130.68 ± 10.38 μM and 179.52 ± 18.89 μM, respectively). Both GPFPLL and LPYPY stably bound to S1 and S1' in DPP-IV, and both demonstrated competitive inhibition of DPP-IV. The inhibition of DPP-IV by GPFPLL and LPYPY after in vitro digestion reached 31.90 % ± 1.80 % and 39.37 % ± 0.90 %, respectively. In a Caco-2 cell experiment, GPFPLL and LPYPY exhibited significant inhibition of DPP-IV, reaching 46.53 % ± 3.48 % and 65.98 % ± 2.87 %, respectively, when the concentration of each peptide was 2 mg/mL. The results of this study suggest that using molecular docking and dynamics simulations to screen novel peptides is an effective approach, and the identified peptides GPFPLL and LPYPY show potential for diabetes management.

Study of the mechanism of non-covalent interactions between chlorogenic acid and soy protein isolate: Multi-spectroscopic, in vitro, and computational docking analyses

This study investigated the interaction mechanism between chlorogenic acid (CA) and soy protein isolate (SPI) through multi-spectroscopic and computational docking and analyzed the changes in its functional properties. The results showed that the interaction of CA with SPI changed its UV and fluorescence absorption, and the fluorescence quenching mechanism was static quenching. At the same time, the secondary structure of the protein was altered, with a reduction in α-helix, β-sheet and β-turn. Computer docking analysis showed that CA binds to SPI through hydrophobic interactions, van der Waals forces, and hydrogen bonding to form a more compact complex. In addition, the dose-dependent enhancement of CA improved the functional properties of the complexes, including foaming, emulsification, and antioxidant properties. This study systematically investigated the mechanism of interaction between CA and SPI, which supports further research on food complex systems containing CA and SPI, as well as the application of the complex.

In Silico Identification and Molecular Mechanism of Novel Tyrosinase Inhibitory Peptides Derived from Nacre of Pinctada martensii

Pearl and nacre powders have been valuable traditional Chinese medicines with whitening properties for thousands of years. We utilized a high-temperature and high-pressure method along with compound enzyme digestion to prepare the enzymatic hydrolysates of nacre powder of Pinctada martensii (NP-PMH). The peptides were identified using LC-MS/MS and screened through molecular docking and molecular dynamics simulations. The interactions between peptides and tyrosinase were elucidated through enzyme kinetics, circular dichroism spectropolarimetry, and isothermal titration calorimetry. Additionally, their inhibitory effects on B16F10 cells were explored. The results showed that a tyrosinase-inhibitory peptide (Ala-His-Tyr-Tyr-Asp, AHYYD) was identified, which inhibited tyrosinase with an IC50 value of 2.012 ± 0.088 mM. The results of the in vitro interactions showed that AHYYD exhibited a mixed-type inhibition of tyrosinase and also led to a more compact enzyme structure. The binding reactions of AHYYD with tyrosinase were spontaneous, leading to the formation of a new set of binding sites on the tyrosinase. The B16F10 cell-whitening assay revealed that AHYYD could reduce the melanin content of the cells by directly inhibiting the activity of intracellular tyrosinase. Additionally, it indirectly affects melanin production by acting as an antioxidant. These results suggest that AHYYD could be widely used as a tyrosinase inhibitor in whitening foods and pharmaceuticals.

Trehalose-conjugated lentil-casein protein complexes prepared by structural interaction: Effects on water solubility and protein digestibility

The two limiting factors for lentil protein utilization are water solubility and digestibility. In this study, we utilized two non-thermal techniques: (1) protein complexation of lentil and casein proteins using the pH-shifting method and (2) protein conjugation with trehalose to produce trehalose-conjugated lentil-casein protein complexes (T-CPs) with enhanced water solubility and digestibility. The protein structure of the T-CPs was analyzed for secondary protein structure, conformation protein, and tertiary protein structure using Fourier-transform infrared, UV, and fluorescence spectroscopies, respectively. The surface hydrophobicity and surface charge of T-CPs solution at pH 7.0 changed significantly (P < 0.05). Using these two non-thermal techniques, the water solubility and digestibility of T-CPs increased significantly (P < 0.05) by 85 to 89 % and 80 to 85 %, respectively. The results of this study suggested that these non-thermal techniques could enhance the surface and protein structure properties, improving water solubility and digestibility.

Mechanistic insight into the mode of inhibition of dietary flavonoids; targeting macrophage migration inhibitory factor

Introduction: The Macrophage Migration Inhibitory Factor (MIF), a key pro-inflammatory mediator, is responsible for modulating immune responses. An array of inflammatory and autoimmune diseases has been linked to the dysregulated activity of MIF. The significance in physiological as well as pathophysiological phenomena underscores the potential of MIF as an attractive target with pharmacological relevance. Extensive research in past has uncovered a number of inhibitors, while the ISO-1, or (S, R)-3-(4-hydroxyphenyl)-4,5-dihydro-5-isoxazole acetic acid methyl ester being recognized as a benchmark standard so far. Recent work by Yang and coworkers identified five promising dietary flavonoids, with superior activity compared to the standard ISO-1. Nevertheless, the exact atomic-level inhibitory mechanism is still elusive. Methods: To improve the dynamic research, and rigorously characterize, and compare molecular signatures of MIF complexes with ISO-1 and flavonoids, principal component analysis (PCA) was linked with molecular dynamics (MD) simulations and binding free energy calculations. Results: The results suggest that by blocking the tautomerase site these small molecule inhibitors could modify the MIF activity by disrupting the intrinsic dynamics in particular functional areas. The stability matrices revealed the average deviation values ranging from 0.27-0.32 nm while the residue level fluctuations indicated that binding of the selected flavonoids confer enhanced stability relative to the ISO-1. Furthermore, the gyration values extracted from the simulated trajectories were found in the range of 1.80-1.83 nm. Discussion: Although all the tested flavonoids demonstrated remarkable results, the one obtained for the potent inhibitors, particularly Morin and Amentoflavone exhibited a good correlation with biological activity. The PCA results featured relatively less variance and constricted conformational landscape than others. The stable ensembles and reduced variation in turns might be the possible reasons for their outstanding performance documented previously. The results from the present exploration provide a comprehensive understanding of the molecular complexes formed by flavonoids and MIF, shedding light on their potential roles and impacts. Future studies on MIF inhibitors may benefit from the knowledge gathered from this investigation.

The recent advances in the approach of artificial intelligence (AI) towards drug discovery

Artificial intelligence (AI) has recently emerged as a unique developmental influence that is playing an important role in the development of medicine. The AI medium is showing the potential in unprecedented advancements in truth and efficiency. The intersection of AI has the potential to revolutionize drug discovery. However, AI also has limitations and experts should be aware of these data access and ethical issues. The use of AI techniques for drug discovery applications has increased considerably over the past few years, including combinatorial QSAR and QSPR, virtual screening, and denovo drug design. The purpose of this survey is to give a general overview of drug discovery based on artificial intelligence, and associated applications. We also highlighted the gaps present in the traditional method for drug designing. In addition, potential strategies and approaches to overcome current challenges are discussed to address the constraints of AI within this field. We hope that this survey plays a comprehensive role in understanding the potential of AI in drug discovery.

Acetylation and Phosphorylation Regulate the Role of Pyruvate Kinase as a Glycolytic Enzyme or a Protein Kinase in Lamb

Protein post-translational modifications (PTMs) play an essential role in meat quality development. However, the effect of specific PTM sites on meat proteins has not been investigated yet. The characteristics of pyruvate kinase M (PKM) were found to exhibit a close correlation with final meat quality, and thus, serine 99 (S99) and lysine 137 (K137) in PKM were mutated to study their effect on PKM function. The structural and functional properties of five lamb PKM variants, including wild-type PKM (wtPKM), PKM_S99D (S99 phosphorylation), PKM_S99A (PKM S99 dephosphorylation), PKM_K137Q (PKM K137 acetylation), and PKM_K137R (PKM K137 deacetylation), were evaluated. The results showed that the secondary structure, tertiary structure, and polymer formation were affected among different PKM variants. In addition, the glycolytic activity of PKM_K137Q was decreased because of its weakened binding with phosphoenolpyruvate. In the PKM_K137R variant, the actin phosphorylation level exhibited a decrease, suggesting a low kinase activity of PKM_K137R. The results of molecular simulation showed a 42% reduction in the interface area between PKM_K137R and actin, in contrast to wtPKM and actin. These findings are significant for revealing the mechanism of how PTMs regulate PKM function and provide a theoretical foundation for the development of precise meat quality preservation technology.