RESUMEN

The adsorption/desorption characteristics of methane (CH4) on moist shale are of great significance for shale gas exploration and production. However, the influence of moisture on CH4 adsorption/desorption under high temperature and pressure conditions, which is consistent to shale reservoirs (burial depths about 3500-4500 m) in China, remained unclear. In this study, quantitative analysis toward moisture dependence of CH4 adsorption/desorption capability on shales was investigated through experimentation and molecular dynamics simulation under moisture contents of 0%, 0.204%, 0.445%, 0.677%, and 0.965%. Results show that with increasing moisture content, the isothermal adsorption capacity of CH4 decrease, and it reaches 36.80% and 10.00% at moisture content of 0.965% in experimentation and simulation, respectively. Simultaneously, the hysteresis index of CH4 desorption increase by 19.64% and 4.52%. The role of water molecules hindering CH4 desorption under low and high moisture content was clarified. At low moisture content, water molecules are mainly adsorbed on the pore walls, thereby reducing the size of the pore throat and hindering CH4 transport pathways. At high moisture content, many water molecules escape from the original adsorption sites and form clusters in the middle of the pores, blocking the pore throats. Meanwhile, CH4 is re-adsorbed onto the exposed adsorption sites of water, which leads to CH4 desorption hysteresis. The results provide valuable insights for shale gas exploration and production under practical water-bearing shale reservoir conditions.

RESUMEN

Elevated blood sugar levels caused by starch digestion was a target for controlling diabetes mellitus. The in vitro and in vivo digestibility of wheat starch was evaluated to find that adding 15 % persimmon leaf extract (PLE) to starch reduced its digestibility by 69.50 % and the peak postprandial blood glucose by 23.63 %. Subsequently, we observed under scanning electron microscopy and atomic force microscopy that the presence of PLE led to the destruction of starch structure and the aggregation of α-glucosidase so as to decrease starch digestion and hinder the binding of starch to α-glucosidase. Through multi-spectral analysis, PLE hindered the clathrate of iodine and starch, and also increased the crystallinity of starch by 48.58 %. For α-glucosidase inhibitory activity (IC50 = 72.49 µg/mL), PLE preferentially occupied the active center of α-glucosidase, changed its fluorescence characteristics and secondary structure through hydrogen bonding and hydrophobic interaction. Moreover, among the 23 potential α-glucosidase inhibitors screened from PLE, combined with molecular simulation, Procyanidin B2 had the strongest inhibitory effect (IC50 = 33.22 µg/mL) and binding energy (-7.09 kcal/mol), which was most effectively inhibitory on digestion. These results indicated the potential of PLE in hypoglycemia targeting both starch and α-glucosidase.

RESUMEN

The behavior of hesperidin methylchalcone (HMC) at the oil/water interface was examined through experimental and molecular simulation methods, and a nano-emulsions based on HMC was subsequently fabricated. The findings indicated that HMC spontaneously aggregated at the oil-water interface, leading to a reduction in interfacial tension and an increase in interfacial thickness. Furthermore, its glycoside and benzene ring showed tendencies to interact with water and medium-chain triglyceride, respectively. The HMC addition amount (w), homogenization times (n) and homogenization pressure (p) significantly influenced the formation of the nano-emulsions. The nano-emulsion with an oil-droplet size of 277.26 ± 13.62 nm was obtained at w = 1.0 %, p = 200 bar, and n = 6. When compared to the Tween 20 nano-emulsion, the HMC nano-emulsion demonstrated superior storage stability, antioxidant activity, and lutein bioaccessibility. It could achieve the slow release of HMC. These findings not only broaden the application range of HMC but also contribute to the advancement of functional nano-emulsions.

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Small-molecule drug design hinges on obtaining co-crystallized ligand-protein structures. Despite AlphaFold2's strides in protein native structure prediction, its focus on apo structures overlooks ligands and associated holo structures. Moreover, designing selective drugs often benefits from the targeting of diverse metastable conformations. Therefore, direct application of AlphaFold2 models in virtual screening and drug discovery remains tentative. Here, we demonstrate an AlphaFold2-based framework combined with all-atom enhanced sampling molecular dynamics and Induced Fit docking, named AF2RAVE-Glide, to conduct computational model-based small-molecule binding of metastable protein kinase conformations, initiated from protein sequences. We demonstrate the AF2RAVE-Glide workflow on three different mammalian protein kinases and their type I and II inhibitors, with special emphasis on binding of known type II kinase inhibitors which target the metastable classical DFG-out state. These states are not easy to sample from AlphaFold2. Here, we demonstrate how with AF2RAVE these metastable conformations can be sampled for different kinases with high enough accuracy to enable subsequent docking of known type II kinase inhibitors with more than 50% success rates across docking calculations. We believe the protocol should be deployable for other kinases and more proteins generally.

Asunto(s)

Descubrimiento de Drogas , Conformación Proteica , Descubrimiento de Drogas/métodos , Simulación del Acoplamiento Molecular , Unión Proteica , Simulación de Dinámica Molecular , Humanos , Inhibidores de Proteínas Quinasas/farmacología , Inhibidores de Proteínas Quinasas/química , Ligandos , Proteínas Quinasas/química , Proteínas Quinasas/metabolismo

RESUMEN

The rise in multi-drug resistant Gram-negative bacterial infections has led to an increased need for 'last-resort' antibiotics such as polymyxins. However, the emergence of polymyxin-resistant strains threatens to bring about a post-antibiotic era. Thus, there is a need to develop new polymyxin-based antibiotics, but a lack of knowledge of the mechanism of action of polymyxins hinders such efforts. It has recently been suggested that polymyxins induce cell lysis of the Gram-negative bacterial inner membrane (IM) by targeting trace amounts of lipopolysaccharide (LPS) localized there. We use multiscale molecular dynamics (MD) including long-timescale coarse-grained (CG) and all-atom (AA) simulations to investigate the interactions of polymyxin B1 (PMB1) with bacterial IM models containing phospholipids (PLs), small quantities of LPS, and IM proteins. LPS was observed to (transiently) phase separate from PLs at multiple LPS concentrations, and associate with proteins in the IM. PMB1 spontaneously inserted into the IM and localized at the LPS-PL interface, where it cross-linked lipid headgroups via hydrogen bonds, sampling a wide range of interfacial environments. In the presence of membrane proteins, a small number of PMB1 molecules formed interactions with them, in a manner that was modulated by local LPS molecules. Electroporation-driven translocation of PMB1 via water-filled pores was favored at the protein-PL interface, supporting the 'destabilizing' role proteins may have within the IM. Overall, this in-depth characterization of PMB1 modes of interaction reveals how small amounts of mislocalized LPS may play a role in pre-lytic targeting and provides insights that may facilitate rational improvement of polymyxin-based antibiotics.

RESUMEN

In this study, the synergistic effect and weak gel mechanism of XG and Gleditsia sinensis polysaccharide (GSP) in different ratios were studied through the rheological properties, microstructure and molecular simulation based on density functional theory (DFT). The results of rheological properties showed that the mixtures formed a weak gel at the concentration of 0.5 % (w/v), with the synergistic impact peaking at a XG/GSP ratio of 3:7. Weak gels produced by XG and GSP had the intersection of G' and G" within the temperature sweep range, and the largest change in the G' slope at a XG/GSP ratio of 3:7. By calculating the interaction energy, it was found that the backbone of XG was more likely to interact with the backbone of GSP. Furthermore, the XG mainchain intersected with the backbone of GSP in a cross shape ("X" shape). As a result, this paper proposed a possible mechanism for the formation of the XG/GSP weak gel, with XG as the main chain and GSP as the grid point, and the main interaction type being hydrogen bonding, with the van der Waals force also involved. The results provide new insight for designing and producing physical gels with specific interactions in food industry.

RESUMEN

This study investigated the influence of Konjac Glucomannan (KGM) with varying degrees of polymerization (DKGMx) on the gelatinization and retrogradation characteristics of wheat starch, providing new insights into starch-polysaccharide interactions. This research uniquely focuses on the effects of DKGMx, utilizing multidisciplinary approaches including Rapid Visco Analysis (RVA), Differential Scanning Calorimetry (DSC), rheological testing, Low-Field Nuclear Magnetic Resonance (LF-NMR), and molecular simulations to assess the effects of DKGMx on gelatinization temperature, viscosity, structural changes post-retrogradation, and molecular interactions. Our findings revealed that higher degrees of polymerization (DP) of DKGMx significantly enhanced starch's pasting viscosity and stability, whereas lower DP reduced viscosity and interfered with retrogradation. High DP DKGMx promoted retrogradation by modifying moisture distribution. Molecular simulations revealed the interplay between low DP DKGMx and starch molecules. These interactions, characterized by increased hydrogen bonds and tighter binding to more starch chains, inhibited starch molecular rearrangement. Specifically, low DP DKGMx established a dense hydrogen bond network with starch, significantly restricting molecular mobility and rearrangement. This study provides new insights into the role of the DP of DKGMx in modulating wheat starch's properties, offering valuable implications for the functional improvement of starch-based foods and advancing starch science.

Asunto(s)

Mananos , Polimerizacion , Almidón , Triticum , Triticum/química , Almidón/química , Viscosidad , Mananos/química , Enlace de Hidrógeno , Reología , Simulación de Dinámica Molecular , Rastreo Diferencial de Calorimetría

RESUMEN

Cell attachment to the extracellular matrix significantly impacts the integrity of tissues and human health. The integrin α5ß1 is a heterodimer of α5 and ß1 subunits and has been identified as a crucial modulator in several human carcinomas. Integrin α5ß1 significantly regulates cell proliferation, angiogenesis, inflammation, tumor metastasis, and invasion. This regulatory role of integrin α5ß1 in tumor metastasis makes it an appealing target for cancer therapy. The majority of the drugs targeting integrin α5ß1 are limited only to clinical trials. In our study, we have performed 94287 compounds screening to determine potential drugs against α5ß1 integrin. We have used ATN-161 as a reference and employed combined bioinformatic methodologies, including molecular modelling, virtual screening, MM-GBSA, cell-line cytotoxicity prediction, ADMET, Density Functional Theory (DFT), Non-covalent Interactions (NCI) and molecular simulation, to identify putative integrin α5ß1 inhibitors. We found Taxifolin, PD133053, and Acebutolol that possess inhibitory activity against α5ß1 integrin and could act as effective drug for the cancer treatment. Taxifolin, PD133053, and Acebutolol exhibited excellent binding to the druggable pocket of integrin α5ß1, and also maintained a unique binding mechanism with extra hydrophobic contacts at molecular level. Overall, our study gives new pharmacological candidates that may act as a potential drug against integrin α5ß1.

RESUMEN

In accordance to the American Heart Association (AHA), cardiovascular diseases (CVDs) are the leading cause of death around the globe, causing more than 19.1 million deaths in 2020. Heart-type fatty acid binding protein (H-FABP) is required for the metabolism of fatty acids (FA) inside cardiomyocytes is reported as a biomarker for myocardial damage. As early as one hour after an Acute myocardial infarction (AMI), H-FABP can be used to detect myocardial ischemia. Thus, H-FABP based detection can reduce the burden on the emergency department. A peptide-based detection system can provide point-of-care diagnostics for CVDs. There is a lot of research being done on peptide-based detection, and it has a lot of potential to help with unmet medical diagnostic needs. A twelve (12) amino acid peptide has been discovered using Phage Display Library Screening. The affinity of peptide with H-FABP and other FABPs has been done using molecular docking and ADMET profile has been done. Molecular docking of small peptides against the target protein can play a crucial role in recognizing peptide binding sites and poses. The docking study was done using the HDOCK server and the visualization of the docked complex was done using Pymol and UCSF chimera. The molecular simulation study of three protein-peptide complexes were done which also validated the binding affinity of peptide with the proteins. The RMSD, RMSF and radius of gyration are also analyzed. The results indicate that H-FABP shows higher level of binding interaction with the peptide having bond length ranging from 2.3 to 3.4 Å. The screened peptide is suitable for H-FABP binding and can be used for prognosis purposes in the heart ischemic conditions.

RESUMEN

The present study uses molecular docking and dynamic simulations to evaluate the inhibitory effect of flavonoid glycosides-based compounds on coronavirus Main protease (Mpro) and RNA polymerase. The Molegro Virtual Docker (MVD) software is utilized to simulate and calculate the binding parameters of compounds with coronavirus. The docking results show that the selected herbal compounds are more effective than those of chemical compounds. It is also revealed that five herbal ligands and two chemical ligands have the best docking scores. Furthermore, a Molecular Dynamics (MD) simulation was conducted for Hesperidin, confirming docking results. Analysis based on different parameters such as Root-mean-square deviation (RMSD), Root mean square fluctuation (RMSF), Radius of gyration (Rg), Solvent accessibility surface area (SASA), and the total number of hydrogen bonds suggests that Hesperidin formed a stable complex with Mpro. Absorption, Distribution, Metabolism, Excretion, And Toxicity (ADMET) analysis was performed to compare Hesperidin and Grazoprevir as potential antiviral medicines, evaluating both herbal and chemical ligand results. According to the study, herbal compounds could be effective on coronavirus and are admissible candidates for developing potential operative anti-viral medicines. Hesperidin was found to be the most acceptable interaction. Grazoprevir is an encouraging candidate for drug development and clinical trials, with the potential to become a highly effective Mpro inhibitor. Compared to RNA polymerase, Mpro showed a greater affinity for bonding with Hesperidin. van der Waals and electrostatic energies dominated, creating a stable Hesperidin-Mpro and Hesperidin-RNA polymerase complex.

RESUMEN

We introduce a novel tree-based method for visualizing molecular conformation sampling. Our method offers enhanced precision in highlighting conformational differences and facilitates the observation of local minimas within proteins fold space. The projection of empirical laboratory data on the tree allows us to create a link between protein conformations and disease relevant data. To demonstrate the efficacy of our approach, we applied it to the ATP-binding cassette subfamily D member 1 (ABCD1) transporter responsible for very long-chain fatty acids (VLCFAs) import into peroxisomes. The genetic disorder called X-linked adrenoleukodystrophy (XALD) is characterized by the accumulation of VLCFA due to pathogenic variants in the ABCD1 gene. Using in silico molecular simulation, we examined the behavior of 16 prevalent mutations alongside the wild-type protein, exploring both inward and outward open forms of the transporter through molecular simulations. We evaluated from resulting trajectories the energy potential related to the ABCD1 interactions with ATP molecules. We categorized XALD patients based on the severity and progression of their disease, providing a unique clinical perspective. By integrating this data into our numerical framework, our study aimed to uncover the molecular underpinnings of XALD, offering new insights into disease progression. As we explored molecular trajectories and conformations resulting from our study, the tree-based method not only contributes valuable insights into XALD but also lays a solid foundation for forthcoming drug design studies. We advocate for the broader adoption of our innovative approach, proposing it as a valuable tool for researchers engaged in molecular simulation studies.

RESUMEN

The capacity of South African Heulandite (HEU) zeolite to remove Pb2+ and Cd2+ ions from aqueous solution was investigated using batch experiments and molecular simulations studies. The effect of different factors on the adsorption of these ions onto the zeolite was investigated; contact time, initial metal ion concentration and the amount of HEU adsorbent. Molecular simulations was done using Monte Carlo and density functional theory. Experimental results obtained indicate that the maximum adsorption for the two ions occur at pH 5 and after 240 min of contact time. The percent removal based on contact time of Pb2+ and Cd2+ ions from water by the heulandite zeolite were 99.7 and 76.7 %, respectively. The adsorption of two metal ions onto the HEU zeolite follows the Langmuir adsorption isotherm. From the molecular simulation findings, the adsorption of Pb2+ ions onto the HEU window is equidistant from the two adjacent oxygen atoms within the HEU structure while the Cd2+ ion is adsorbed in the upper left side of the 8-ring HEU window. It was observed that the performance of the zeolite can significantly be improved by doping with germanium, aluminum, thallium indium, and sodium cations. These results indicate that the application of HEU zeolite as an adsorbent holds a great promise in heavy metal removal from aqueous solutions.

RESUMEN

Due to the multiple influences of unique physicochemical properties of helium, petrographic characteristics and temperature and pressure conditions, little is known about the helium adsorption behaviors in minerals and rocks at geological conditions. Based on the grand canonical Monte Carlo simulations, this study revealed the adsorption characteristics of pure helium and the competitive adsorption of binary mixtures with different proportions of methane and helium under geological temperature and pressure conditions in quartz slit model. Molecular simulation of pure helium shows that physical adsorption of helium exists in mineral surfaces, which indicates a preservation mechanism of helium in helium source rocks. Binary mixtures simulations indicate that the adsorption capacity of methane in quartz is stronger than that of helium, and the competitive adsorption of methane increases with decreasing burial depth. This means that during the upwards migration processes of natural gas, the adsorbed helium that distributed in the migration pathway will be gradually displaced by methane, then concentrate in the hydrocarbon gases and subsequently accumulate together in favorable traps to form helium-rich natural gas reservoirs. Our results provide a molecular-scale insight into the preservation and accumulation of helium in helium source rocks and are significant for assessing the helium resource potential.

RESUMEN

Lycium ruthenicum Murr. is mainly distributed in the northwest region of China and its berries are rich in anthocyanin. This study evaluated the hypoglycaemic activity of the anthocyanin-enriched fraction (AEF) of L. ruthenicum Murr. on α-glucosidase in vivo and in vitro. Overall, 10 anthocyanins were identified via UPLC-Triple-TOF-MS/MS. The AEF exhibited strong inhibitory activity against α-glucosidase, with an IC50 value of 4.468 mg/mL. It behaved as a reversible, mixed-type inhibitor. Molecular docking and dynamic results indicated that the compounds in AEF interacted with enzymes primarily through van der Waals and hydrogen bond and the complex system was stable. The postprandial blood glucose and area under the curve of diabetic mice was significantly decreased by AEF in the carbohydrate tolerance experiments. The results indicate that the AEF from L. ruthenicum Murr. berries could be as a promising food supplement for managing blood sugar levels in patients with diabetes mellitus.

Asunto(s)

Antocianinas , Frutas , Hipoglucemiantes , Lycium , Extractos Vegetales , Espectrometría de Masas en Tándem , Lycium/química , Frutas/química , Animales , Hipoglucemiantes/química , Hipoglucemiantes/farmacología , Antocianinas/química , Antocianinas/farmacología , Ratones , Extractos Vegetales/química , Extractos Vegetales/farmacología , Cromatografía Líquida de Alta Presión , Masculino , Humanos , alfa-Glucosidasas/química , alfa-Glucosidasas/metabolismo , Glucemia/metabolismo , Simulación del Acoplamiento Molecular , Inhibidores de Glicósido Hidrolasas/química , Inhibidores de Glicósido Hidrolasas/farmacología

RESUMEN

The aberrant fibrillization of huntingtin exon 1 (Httex1) characterized by an expanded polyglutamine (polyQ) tract is a defining feature of Huntington's disease, a neurodegenerative disorder. Recent investigations underscore the involvement of a small EDRK-rich factor 1a (SERF1a) in promoting Httex1 fibrillization through interactions with its N terminus. By establishing an integrated approach with size-exclusion-column-based small- and wide-angle X-ray scattering (SEC-SWAXS), NMR, and molecular simulations using Rosetta, the analysis here reveals a tight binding of two NT17 fragments of Httex1 (comprising the initial 17 amino acids at the N terminus) to the N-terminal region of SERF1a. In contrast, examination of the complex structure of SERF1a with a coiled NT17-polyQ peptide (33 amino acids in total) indicates sparse contacts of the NT17 and polyQ segments with the N-terminal side of SERF1a. Furthermore, the integrated SEC-SWAXS and molecular-simulation analysis suggests that the coiled NT17 segment can transform into a helical conformation when associated with a polyQ segment exhibiting high helical content. Intriguingly, NT17-polyQ peptides with enhanced secondary structures display diminished interactions with SERF1a. This insight into the conformation-dependent binding of NT17 provides clues to a catalytic association mechanism underlying SERF1a's facilitation of Httext1 fibrillization.

Asunto(s)

Proteína Huntingtina , Péptidos , Proteína Huntingtina/genética , Proteína Huntingtina/química , Proteína Huntingtina/metabolismo , Péptidos/química , Péptidos/metabolismo , Péptidos/genética , Humanos , Exones/genética , Unión Proteica , Enfermedad de Huntington/genética , Enfermedad de Huntington/metabolismo , Simulación de Dinámica Molecular , Espectroscopía de Resonancia Magnética , Difracción de Rayos X

RESUMEN

Mycoplasma pulmonis (M. pulmonis) is an emerging respiratory infection commonly linked to prostate cancer, and it is classified under the group of mycoplasmas. Improved management of mycoplasma infections is essential due to the frequent ineffectiveness of current antibiotic treatments in completely eliminating these pathogens from the host. The objective of this study is to design and construct effective and protective vaccines guided by structural proteomics and machine learning algorithms to provide protection against the M. pulmonis infection. Through a thorough examination of the entire proteome of M. pulmonis, four specific targets Membrane protein P80, Lipoprotein, Uncharacterized protein and GGDEF domain-containing protein have been identified as appropriate for designing a vaccine. The proteins underwent mapping of cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL) (IFN)-γ ±, and B-cell epitopes using artificial and recurrent neural networks. The design involved the creation of mRNA and peptide-based vaccine, which consisted of 8 CTL epitopes associated by GGS linkers, 7 HTL (IFN-positive) epitopes, and 8 B-cell epitopes joined by GPGPG linkers. The vaccine designed exhibit antigenic behavior, non-allergenic qualities, and exceptional physicochemical attributes. Structural modeling revealed that correct folding is crucial for optimal functioning. The coupling of the MEVC and Toll-like Receptors (TLR)1, TLR2, and TLR6 was examined through molecular docking experiments. This was followed by molecular simulation investigations, which included binding free energy estimations. The results indicated that the dynamics of the interaction were stable, and the binding was strong. In silico cloning and optimization analysis revealed an optimized sequence with a GC content of 49.776 % and a CAI of 0.982. The immunological simulation results showed strong immune responses, with elevated levels of active and plasma B-cells, regulatory T-cells, HTL, and CTL in both IgM+IgG and secondary immune responses. The antigen was completely cleared by the 50th day. This study lays the foundation for creating a potent and secure vaccine candidate to combat the newly identified M. pulmonis infection in people.

Asunto(s)

Vacunas Bacterianas , Epítopos de Linfocito B , Epítopos de Linfocito T , Aprendizaje Automático , Infecciones por Mycoplasma , Proteómica , Vacunas Bacterianas/inmunología , Infecciones por Mycoplasma/prevención & control , Infecciones por Mycoplasma/inmunología , Proteómica/métodos , Animales , Epítopos de Linfocito T/inmunología , Epítopos de Linfocito B/inmunología , Linfocitos T Citotóxicos/inmunología , Humanos , Proteínas Bacterianas/inmunología , Ratones , Simulación del Acoplamiento Molecular , Mapeo Epitopo/métodos , Antígenos Bacterianos/inmunología

RESUMEN

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.

Asunto(s)

Quitosano , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Oligosacáridos , Unión Proteica , SARS-CoV-2 , Humanos , Oligosacáridos/química , Oligosacáridos/farmacología , SARS-CoV-2/efectos de los fármacos , Células HEK293 , Quitosano/química , Quitosano/análogos & derivados , Quitosano/farmacología , Glicoproteína de la Espiga del Coronavirus/química , Glicoproteína de la Espiga del Coronavirus/metabolismo , Glicoproteína de la Espiga del Coronavirus/genética , Antivirales/farmacología , Antivirales/química , COVID-19/virología , Sitios de Unión , Quitina/análogos & derivados , Quitina/química , Quitina/farmacología , Enzima Convertidora de Angiotensina 2/química , Enzima Convertidora de Angiotensina 2/metabolismo , Dominios Proteicos , Tratamiento Farmacológico de COVID-19

RESUMEN

The combination of food chemistry and computational simulation has brought many impacts to food research, moving from experimental chemistry to computer chemistry. This paper will systematically review in detail the important role played by computational simulations in the development of the molecular structure of food, mainly from the atomic, molecular, and multicomponent dimension. It will also discuss how different computational chemistry models can be constructed and analyzed to obtain reliable conclusions. From the calculation principle to case analysis, this paper focuses on the selection and application of quantum mechanics, molecular mechanics and coarse-grained molecular dynamics in food chemistry research. Finally, experiments and computations of food chemistry are compared and summarized to obtain the best balance between them. The above review and outlook will provide an important reference for the intersection of food chemistry and computational chemistry, and is expected to provide innovative thinking for structural research in food chemistry.

Asunto(s)

Análisis de los Alimentos , Simulación de Dinámica Molecular , Análisis de los Alimentos/métodos , Teoría Cuántica , Química Computacional , Simulación por Computador

RESUMEN

OBJECTIVE: This study aimed to compare the effects of ß-sitosterol nanoparticles (BETNs) and ß-sitosterol (BET) on cognitive impairment, oxidative stress, and inflammation in a myocardial infarction (MI) rat model using in silico and in vivo methods. METHODS: ß-Sitosterol (BET) and myeloperoxidase (MPO) ligand-receptor binding affinities were evaluated using Autodock Vina for docking and Gromacs for dynamics simulations. BET nanoparticles, prepared via solvent evaporation, had their size confirmed by a nanoparticle analyzer. ISO-induced cognitive impairment in rats was assessed through Morris water maze and Cook's pole climbing tests. Oxidative stress, inflammation, and cardiac injury were evaluated by measuring GSH, SOD, MDA, MPO, CkMB, LDH, lipid profiles, and ECGs. Histopathology of the CA1 hippocampus and myocardial tissue was performed using H&E staining. RESULTS: In silico analyses revealed strong binding affinities between BET and MPO, suggesting BET's potential anti-inflammatory effect. BETN (119.6 ± 42.6 nm; PDI: 0.809) significantly improved MI-induced cognitive dysfunction in rats (p < 0.001 ***), increased hippocampal GSH (p < 0.01 **) and SOD (p < 0.01 **) levels, and decreased hippocampal MDA (p < 0.05 *) and MPO levels (p < 0.01 **). BETNs also elevated cardiac GSH (p < 0.01 **) and SOD (p < 0.01 **) levels and reduced cardiac MPO (p < 0.01 **), CkMB (p < 0.001 **) and LDH (p < 0.001 **) levels. It restored lipid profiles, normalized ECG patterns, and improved histology in the hippocampal CA1 region and myocardium. CONCLUSIONS: Compared with BET treatment, BETNs were more effective in improving cognitive impairment, oxidative damage, and inflammation in MI rats, suggesting its potential in treating cognitive dysfunction and associated pathological changes in MI.

RESUMEN

Cancer poses a significant global public health challenge, with commonly used adjuvant or neoadjuvant chemotherapy often leading to adverse side effects and drug resistance. Therefore, advancing cancer treatment necessitates the ongoing development of novel anticancer agents with diverse structures and mechanisms of action. Natural products remain crucial in the process of drug discovery, serving as a primary source for pharmaceutical leads and therapeutic advancements. Triterpenoids are particularly compelling due to their complex structures and wide array of biological activities. Recent research has demonstrated that naturally occurring triterpenes and their derivatives have the potential to serve as promising candidates for new drug development. This review aims to comprehensively explore the anticancer properties of triterpenoids and their synthetic analogs, with a focus on recent advancements. Various aspects, such as synthesis, phytochemistry, and molecular simulation for structure-activity relationship analyses, are summarized. It is anticipated that triterpenoid derivatives will emerge as notable anticancer agents following further investigation into their mechanisms of action and in vivo studies.