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1.
J Food Sci ; 89(7): 4109-4122, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38957103

RESUMO

The elucidation of the interaction mechanism between phospholipids and milk proteins within emulsions is pivotal for comprehending the properties of infant formula fat globules. In this study, multispectral methods and molecular docking were employed to explore the relationship between phosphatidylcholine (PC) and whey protein isolate (WPI). Observations indicate that the binding constant, alongside thermodynamic parameters, diminishes as temperature ascends, hinting at a predominantly static quenching mechanism. Predominantly, van der Waals forces and hydrogen bonds constitute the core interactions between WPI and PC. This assertion is further substantiated by Fourier transform infrared spectroscopy, which verifies PC's influence on WPI's secondary structure. A detailed assessment of thermodynamic parameters coupled with molecular docking reveals that PC predominantly adheres to specific sites within α-lactalbumin, ß-lactoglobulin, and bovine serum albumin, propelled by a synergy of hydrophobic interactions, hydrogen bonding, and van der Waals forces, with binding energies noted at -5.59, -6.71, and -7.85 kcal/mol, respectively. An increment in PC concentration is observed to amplify the emulsification properties of WPI whilst concurrently diminishing the zeta potential. This study establishes a theoretical foundation for applying the PC-WPI interaction mechanism in food.


Assuntos
Ligação de Hidrogênio , Interações Hidrofóbicas e Hidrofílicas , Simulação de Acoplamento Molecular , Fosfatidilcolinas , Termodinâmica , Proteínas do Soro do Leite , Proteínas do Soro do Leite/química , Fosfatidilcolinas/química , Espectroscopia de Infravermelho com Transformada de Fourier/métodos , Lactoglobulinas/química , Lactoglobulinas/metabolismo , Emulsões/química , Lactalbumina/química , Lactalbumina/metabolismo , Soroalbumina Bovina/química , Fórmulas Infantis/química
2.
Chem Biol Drug Des ; 104(1): e14576, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38969623

RESUMO

Intestinal absorption of compounds is significant in drug research and development. To evaluate this efficiently, a method combining mathematical modeling and molecular simulation was proposed, from the perspective of molecular structure. Based on the quantitative structure-property relationship study, the model between molecular structure and their apparent permeability coefficients was successfully constructed and verified, predicting intestinal absorption of drugs and interpreting decisive structural factors, such as AlogP98, Hydrogen bond donor and Ellipsoidal volume. The molecules with strong lipophilicity, less hydrogen bond donors and receptors, and small molecular volume are more easily absorbed. Then, the molecular dynamics simulation and molecular docking were utilized to study the mechanism of differences in intestinal absorption of drugs and investigate the role of molecular structure. Results indicated that molecules with strong lipophilicity and small volume interacted with the membrane at a lower energy and were easier to penetrate the membrane. Likewise, they had weaker interaction with P-glycoprotein and were easier to escape from it and harder to export from the body. More in, less out, is the main reason these molecules absorb well.


Assuntos
Ligação de Hidrogênio , Absorção Intestinal , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Relação Quantitativa Estrutura-Atividade , Humanos , Estrutura Molecular , Preparações Farmacêuticas/metabolismo , Preparações Farmacêuticas/química , Membro 1 da Subfamília B de Cassetes de Ligação de ATP/metabolismo , Membro 1 da Subfamília B de Cassetes de Ligação de ATP/química , Interações Hidrofóbicas e Hidrofílicas , Permeabilidade
3.
Proc Natl Acad Sci U S A ; 121(31): e2407501121, 2024 Jul 30.
Artigo em Inglês | MEDLINE | ID: mdl-39042697

RESUMO

This study explores the impact of electrostatic interactions and hydrogen bonding on tear film stability, a crucial factor for ocular surface health. While mucosal and meibomian layers have been extensively studied, the role of electrolytes in the aqueous phase remains unclear. Dry eye syndrome, characterized by insufficient tear quantity or quality, is associated with hyperosmolality, making electrolyte composition an important factor that might impact tear stability. Using a model buffer solution on a silica glass dome, we simulated physiologically relevant tear film conditions. Sodium chloride alone induced premature dewetting through salt crystal nucleation. In contrast, trace amounts of solutes with hydroxyl groups (sodium phosphate dibasic, potassium phosphate monobasic, and glucose) exhibited intriguing phenomena: quasi-stable films, solutal Marangoni-driven fluid influx increasing film thickness, and viscous fingering due to Saffman-Taylor instability. These observations are rationalized by the association of salt solutions with increased surface tension and the propensity of hydroxyl-group-containing solutes to engage in significant hydrogen bonding, altering local viscosity. This creates a viscosity contrast between the bulk buffer solution and the film region. Moreover, these solutes shield the glass dome, counteracting sodium chloride crystallization. These insights not only advance our understanding of tear film mechanics but also pave the way for predictive diagnostics in dry eye syndrome, offering a robust platform for personalized medical interventions based on individual tear film composition.


Assuntos
Eletrólitos , Ligação de Hidrogênio , Lágrimas , Lágrimas/química , Eletrólitos/química , Humanos , Viscosidade , Cloreto de Sódio/química , Fosfatos/química , Tensão Superficial , Eletricidade Estática , Síndromes do Olho Seco/metabolismo , Molhabilidade , Compostos de Potássio
4.
J Phys Chem B ; 128(28): 6853-6865, 2024 Jul 18.
Artigo em Inglês | MEDLINE | ID: mdl-38981040

RESUMO

This work presents a study on the effects of periodic boundary conditions (PBC) on the energetic/structural properties and hydrogen bond dynamics (HB) using molecular dynamics (MD) simulations of peptide membranes composed of alanine and histidine. Our results highlight that simulations using small surface areas for the peptide membrane may result in nonconvergent values for membrane properties, which are only observed in regions simulated at a certain distance from the PBCs. Specifically, regarding hydrogen bonds, a property pervasive in peptide membranes, our findings indicate a significant increase in the lifetime of these interactions, reaching values ∼19% higher when observed in structures free from PBCs. For peptide mobility in these nanomembranes, our results compare regions simulated directly under the influence of PBCs with regions free from these conditions, emphasizing greater mobility of amino acid psi/phi angles in the latter model.


Assuntos
Ligação de Hidrogênio , Simulação de Dinâmica Molecular , Nanoestruturas , Peptídeos , Nanoestruturas/química , Peptídeos/química , Histidina/química , Alanina/química
5.
J Agric Food Chem ; 72(29): 16438-16448, 2024 Jul 24.
Artigo em Inglês | MEDLINE | ID: mdl-38981019

RESUMO

Steviol glycosides (SGs) are a natural sweetener widely used in the food and beverage industry, but the low solubility and stability of SG aqueous solutions greatly limit their application performance, especially in liquid formulations. In this work, we explore the solubility behavior of rebaudioside A (Reb A) in water, a major component of SGs, with the aim of clarifying the underlying mechanisms of the solubility and stability constraints of SGs, as well as the impact on their multifunctional properties. We demonstrate for the first time that Reb A exhibits hierarchical self-assembly in solutions, forming spherical micelles first when the concentration exceeds its critical micelle concentration (5.071 mg/mL), which then further assemble into large rod-like aggregates. The formation of such large Reb A aggregates is mainly dominated by hydrogen bonding and short-range Coulomb interaction energy, thus leading to the low solubility and precipitation of Reb A solutions. Surprisingly, aggregated Reb A structures display significantly improved organoleptic properties, revealing that self-aggregation can be developed as a simple, efficient, and green strategy for improving the taste profile of SGs. Additionally, the self-aggregation of Reb A at high concentrations impairs active encapsulation and also affects its interfacial and emulsifying properties.


Assuntos
Diterpenos do Tipo Caurano , Glicosídeos , Solubilidade , Edulcorantes , Diterpenos do Tipo Caurano/química , Edulcorantes/química , Glicosídeos/química , Água/química , Micelas , Ligação de Hidrogênio , Paladar , Glucosídeos/química , Stevia/química , Soluções/química
6.
Phys Chem Chem Phys ; 26(29): 19775-19786, 2024 Jul 24.
Artigo em Inglês | MEDLINE | ID: mdl-38984923

RESUMO

The Leucine-rich repeat kinase 2 (LRRK2) target has been identified as a promising drug target for Parkinson's disease (PD) treatment. This study focuses on optimizing the activity of LRRK2 inhibitors using alchemical relative binding free energy (RBFE) calculations. Initially, we assessed various free energy calculation methods across different LRRK2 kinase inhibitor scaffolds. The results indicate that alchemical free energy calculations are promising for prospective predictions on LRRK2 inhibitors, especially for the aminopyrimidine scaffold with an RMSE of 1.15 kcal mol-1 and Rp of 0.83. Following this, we optimized a potent LRRK2 kinase inhibitor identified from previous virtual screenings, featuring a novel scaffold. Guided by RBFE predictions using alchemical methods, this optimization led to the discovery of compound LY2023-001. This compound, with a [1,2,4]triazolo[5,6-b]indole scaffold, exhibited enhanced inhibitory activity against G2019S LRRK2 (IC50 = 12.9 nM). Molecular dynamics (MD) simulations revealed that LY2023-001 formed stable hydrogen bonds with Glu1948, and Ala1950 in the G2019S LRRK2 protein. Additionally, its phenyl substituents engage in strong electrostatic interactions with Lys1906 and van der Waals interactions with Leu1885, Phe1890, Val1893, Ile1933, Met1947, Leu1949, Leu2001, Ala2016, and Asp2017. Our findings underscore the potential of computational methods in the successful optimization of small molecules, offering important insights for the development of novel LRRK2 inhibitors.


Assuntos
Serina-Treonina Proteína Quinase-2 com Repetições Ricas em Leucina , Simulação de Dinâmica Molecular , Inibidores de Proteínas Quinases , Termodinâmica , Serina-Treonina Proteína Quinase-2 com Repetições Ricas em Leucina/antagonistas & inibidores , Serina-Treonina Proteína Quinase-2 com Repetições Ricas em Leucina/metabolismo , Serina-Treonina Proteína Quinase-2 com Repetições Ricas em Leucina/química , Inibidores de Proteínas Quinases/química , Inibidores de Proteínas Quinases/farmacologia , Humanos , Ligação de Hidrogênio , Ligação Proteica , Estrutura Molecular , Simulação de Acoplamento Molecular
7.
Molecules ; 29(13)2024 Jun 21.
Artigo em Inglês | MEDLINE | ID: mdl-38998901

RESUMO

Long-range HNCO NMR spectra for proteins show crosspeaks due to 1JNC', 2JNC', 3JNCγ, and h3JNC' couplings. The h3JNC' couplings are transmitted through hydrogen bonds and their sizes are correlated to hydrogen bond lengths. We collected long-range HNCO data at a series of temperatures for four protein structures. P22i and CUS-3i are six-stranded beta-barrel I-domains from phages P22 and CUS-3 that share less than 40% sequence identity. The cis and trans states of the C-terminal domain from pore-forming toxin hemolysin ΙΙ (HlyIIC) arise from the isomerization of a single G404-P405 peptide bond. For P22i and CUS-3i, hydrogen bonds detected by NMR agree with those observed in the corresponding domains from cryoEM structures of the two phages. Hydrogen bond lengths derived from the h3JNC' couplings, however, are poorly conserved between the distantly related CUS-3i and P22i domains and show differences even between the closely related cis and trans state structures of HlyIIC. This is consistent with hydrogen bond lengths being determined by local differences in structure rather than the overall folding topology. With increasing temperature, hydrogen bonds typically show an apparent increase in length that has been attributed to protein thermal expansion. Some hydrogen bonds are invariant with temperature, however, while others show apparent decreases in length, suggesting they become stabilized with increasing temperature. Considering the data for the three proteins in this study and previously published data for ubiquitin and GB3, lowered protein folding stability and cooperativity corresponds with a larger range of temperature responses for hydrogen bonds. This suggests a partial uncoupling of hydrogen bond energetics from global unfolding cooperativity as protein stability decreases.


Assuntos
Ligação de Hidrogênio , Temperatura , Ressonância Magnética Nuclear Biomolecular , Modelos Moleculares , Estabilidade Proteica , Conformação Proteica , Proteínas/química , Espectroscopia de Ressonância Magnética/métodos , Proteínas Hemolisinas/química
8.
Environ Sci Pollut Res Int ; 31(32): 45204-45216, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38958860

RESUMO

Ionic polymers functionalized with hydroxyl, carboxyl, and amino groups can enhance the catalytic activity of catalysts. However, the straightforward preparation of bifunctional ionic polymers containing abundant ionic active sites and hydrogen bond donors remains challenging. In this study, a series of porous ionic polymers (BZIs) containing different hydrogen bond donors (-NH2, -OH, -COOH) were prepared through a simple one-pot Friedel-Crafts alkylation using benzimidazole derivatives and benzyl bromide. The structures and properties of BZIs were characterized by various techniques such as Fourier-transform infrared spectroscopy, X-ray photoelectron spectroscopy, solid-state nuclear magnetic resonance, and scanning electron microscopy. Among the prepared catalysts (BZI-NH2, BZI-OH, and BZI-COOH), BZI-NH2 exhibited the highest catalytic activity and recyclability, achieving a yield of 97% in the CO2 cycloaddition. The synergistic effect of Br-, hydrogen bond donors (-NH-, -NH2), and N+ in BZI-NH2 was found to contribute to its superior catalytic performance. DFT calculations were employed to study the effect of hydrogen bonds, Br-, and N+ in BZI-NH2 and BZI-OH on the CO2 cycloaddition. Using BZI-NH2 as an example, a mechanism was proposed for the synergistic effect between amino groups and bromide ions in catalyzing the CO2 cycloaddition reaction.


Assuntos
Benzimidazóis , Dióxido de Carbono , Reação de Cicloadição , Benzimidazóis/química , Catálise , Dióxido de Carbono/química , Ligação de Hidrogênio , Polímeros/química
9.
J Phys Chem B ; 128(28): 6670-6683, 2024 Jul 18.
Artigo em Inglês | MEDLINE | ID: mdl-38982772

RESUMO

DNA photolyase targets the primary ultraviolet (UV)-induced DNA lesion─cyclobutane pyrimidine dimer (CPD), attaches to it, and catalyzes its dissociation. The catalytic mechanism of DNA photolyase and the role of the conserved residue E283 remain subjects of debate. This study employs two-dimensional potential energy surface maps and minimum free energy paths calculated at the ωB97XD/6-31G/MM level to elucidate these mechanisms. Results suggest that the catalytic process follows a sequential, stepwise reaction in which the C5-C5 and C6-C6 bonds are cleaved in order, facilitated by a protonated E283. Activation free energies for these cleavages are calculated at 4.4 and 4.2 kcal·mol-1, respectively. Protonation of E283 reduces electrostatic repulsion with CPD and forms dual hydrogen bonds with it and provides better solvation, stabilizing the CPD radical anion, particularly during intermediate state. This stabilization renders the initial splitting step exergonic, slows reverse reactions of the C5-C5 bond cleavage and electron transfer, and ensures a high quantum yield. Furthermore, the protonation state of E283 significantly affects the type of bond cleavage. Other residues in the active site were also investigated for their roles in the mechanism.


Assuntos
Teoria da Densidade Funcional , Prótons , Dímeros de Pirimidina , Dímeros de Pirimidina/química , Desoxirribodipirimidina Fotoliase/química , Desoxirribodipirimidina Fotoliase/metabolismo , Termodinâmica , Simulação de Dinâmica Molecular , Ligação de Hidrogênio , Ciclização
10.
J Chem Theory Comput ; 20(14): 6369-6387, 2024 Jul 23.
Artigo em Inglês | MEDLINE | ID: mdl-38991114

RESUMO

G protein-coupled receptors (GPCR) are responsible for modulating various physiological functions and are thus related to the pathophysiology of different diseases. Being potential therapeutic targets, multiple computational methodologies have been developed to analyze their behavior and interactions with other species. The solvent, on the other hand, has received much less attention. In this work, we analyzed the effect of four explicit water models on the structure and interactions of the GPR40 receptor in its apo form. We employed the rigid SPC/E and TIP4P models, and their flexible versions, the FBA/ϵ and TIP4P/ϵflex. We explored the structural changes and their correlation with some bulk dynamic properties of water. Our results showed an adverse effect on the conservation of the secondary structure of the receptor with all the models due to the breaking of the intramolecular hydrogen bond network, being more evident for the TIP4P models. Notably, all four models brought the receptor to states similar to the active one, modifying the intracellular part of the TM5 and TM6 domains in a "hinge" type movement, allowing the opening of the structure. Regarding the dynamic properties, the rigid models showed results comparable to those obtained in other studies on membrane systems. However, flexible models exhibit disparities in the molecular representation of systems. Surprisingly, the FBA/ϵ model improves the molecular picture of several properties, even though their agreement with bulk diffusion is poorer. These findings reinforce our idea that exploring other water models or improving the current ones, to better represent the membrane interface, can lead to a positive impact on the description of the signal transduction mechanisms and the search of new drugs by targeting these receptors.


Assuntos
Receptores Acoplados a Proteínas G , Solventes , Água , Receptores Acoplados a Proteínas G/química , Receptores Acoplados a Proteínas G/metabolismo , Água/química , Solventes/química , Humanos , Simulação de Dinâmica Molecular , Ligação de Hidrogênio
11.
Top Curr Chem (Cham) ; 382(3): 27, 2024 Jul 20.
Artigo em Inglês | MEDLINE | ID: mdl-39033235

RESUMO

Supramolecular polymers are polymeric materials of monomeric fragments, held jointly by reversible and directional non-covalent interactions such as multiple hydrogen-bonding, charge transfer effects, host-guest interactions, metal coordination, and aromatic stacking. This review article on the Hamilton-based supramolecular polymers aims to shed light on the molecular recognition achievements by the Hamilton-based polymeric systems, evaluate Hamilton receptor's future prospects, and capitalize its potential applications in supramolecular chemistry. To the best of our knowledge, this is the first elaborative and sole manuscript in which polymeric Hamilton receptors are being exposed in detail. The first portion of this manuscript is related to the importance and urgency of polymers along with the historic background of Hamilton receptors. The middle section discloses the potential applications of Hamilton-type receptors in various fields, e.g., dendrimers, mechanically polymeric rotaxanes, and self-assemblies. The final section of the manuscript discloses the future aspects and the importance of novel polymer-based Hamilton-type receptors in the modern era. We believe that this first review in this emerging yet immature field will be useful to inspire scientists around the world to find the unseen future prospects, thereby boosting the field related to this valued artificial receptor in the province of supramolecular chemistry and also in other domains of scientific fields and technology, as well.


Assuntos
Polímeros , Polímeros/química , Substâncias Macromoleculares/química , Rotaxanos/química , Dendrímeros/química , Estrutura Molecular , Receptores Artificiais/química , Receptores Artificiais/metabolismo , Ligação de Hidrogênio
12.
Proc Natl Acad Sci U S A ; 121(29): e2408156121, 2024 Jul 16.
Artigo em Inglês | MEDLINE | ID: mdl-38980907

RESUMO

After ATP-actin monomers assemble filaments, the ATP's [Formula: see text]-phosphate is hydrolyzedwithin seconds and dissociates over minutes. We used all-atom molecular dynamics simulations to sample the release of phosphate from filaments and study residues that gate release. Dissociation of phosphate from Mg2+ is rate limiting and associated with an energy barrier of 20 kcal/mol, consistent with experimental rates of phosphate release. Phosphate then diffuses within an internal cavity toward a gate formed by R177, as suggested in prior computational studies and cryo-EM structures. The gate is closed when R177 hydrogen bonds with N111 and is open when R177 forms a salt bridge with D179. Most of the time, interactions of R177 with other residues occlude the phosphate release pathway. Machine learning analysis reveals that the occluding interactions fluctuate rapidly, underscoring the secondary role of backdoor gate opening in Pi release, in contrast with the previous hypothesis that gate opening is the primary event.


Assuntos
Citoesqueleto de Actina , Trifosfato de Adenosina , Simulação de Dinâmica Molecular , Fosfatos , Fosfatos/metabolismo , Fosfatos/química , Citoesqueleto de Actina/metabolismo , Citoesqueleto de Actina/química , Trifosfato de Adenosina/metabolismo , Actinas/metabolismo , Actinas/química , Ligação de Hidrogênio , Magnésio/metabolismo , Magnésio/química , Microscopia Crioeletrônica
13.
Protein Sci ; 33(8): e5100, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-39022909

RESUMO

Cholinesterases are well-known and widely studied enzymes crucial to human health and involved in neurology, Alzheimer's, and lipid metabolism. The protonation pattern of active sites of cholinesterases influences all the chemical processes within, including reaction, covalent inhibition by nerve agents, and reactivation. Despite its significance, our comprehension of the fine structure of cholinesterases remains limited. In this study, we employed enhanced-sampling quantum-mechanical/molecular-mechanical calculations to show that cholinesterases predominantly operate as dynamic mixtures of two protonation states. The proton transfer between two non-catalytic glutamate residues follows the Grotthuss mechanism facilitated by a mediator water molecule. We show that this uncovered complexity of active sites presents a challenge for classical molecular dynamics simulations and calls for special treatment. The calculated proton transfer barrier of 1.65 kcal/mol initiates a discussion on the potential existence of two coupled low-barrier hydrogen bonds in the inhibited form of butyrylcholinesterase. These findings expand our understanding of structural features expressed by highly evolved enzymes and guide future advances in cholinesterase-related protein and drug design studies.


Assuntos
Butirilcolinesterase , Domínio Catalítico , Simulação de Dinâmica Molecular , Prótons , Butirilcolinesterase/química , Butirilcolinesterase/metabolismo , Humanos , Ligação de Hidrogênio , Acetilcolinesterase/química , Acetilcolinesterase/metabolismo , Colinesterases/química , Colinesterases/metabolismo
14.
AAPS J ; 26(4): 83, 2024 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-39009955

RESUMO

Salts of weakly basic drugs can partially dissociate in formulations, to give basic drugs and counter acids. The aim of the present study was to clarify the effect of physicochemical properties on the basic drug-acid-polymer interactions and salt-polymer miscibility, and to explain the influence mechanism at the molecular level. Six maleate salts with different physicochemical properties were selected and PVA was used as the film forming material. The relationship between the physicochemical properties and the miscibility was presented with multiple linear regression analysis. The existence state of salts in formulations were determined by XRD and Raman imaging. The stability of salts was characterized by NMR and XPS. The intermolecular interactions were investigated by FTIR and NMR. The results showed that the salt-PVA miscibility was related to polar surface area of salts and Tg of free bases, which represented hydrogen bond interaction and solubility potential. The basic drug-acid-PVA intermolecular interactions determined the existence state and bonding pattern of the three molecules. Meanwhile, the decrease of the stability after formulation increased the number of free bases in orodispersible films, which in turn affected the miscibility with PVA. The study provided references for the rational design of PVA based orodispersible films.


Assuntos
Álcool de Polivinil , Solubilidade , Álcool de Polivinil/química , Administração Oral , Estabilidade de Medicamentos , Maleatos/química , Química Farmacêutica/métodos , Ligação de Hidrogênio , Espectroscopia de Infravermelho com Transformada de Fourier , Difração de Raios X
15.
Nat Commun ; 15(1): 5619, 2024 Jul 04.
Artigo em Inglês | MEDLINE | ID: mdl-38965213

RESUMO

The sigma-1 receptor (σ1R) is a non-opioid membrane receptor, which responds to a diverse array of synthetic ligands to exert various pharmacological effects. Meanwhile, candidates for endogenous ligands of σ1R have also been identified. However, how endogenous ligands bind to σ1R remains unknown. Here, we present crystal structures of σ1R from Xenopus laevis (xlσ1R) bound to two endogenous neurosteroid ligands, progesterone (a putative antagonist) and dehydroepiandrosterone sulfate (DHEAS) (a putative agonist), at 2.15-3.09 Å resolutions. Both neurosteroids bind to a similar location in xlσ1R mainly through hydrophobic interactions, but surprisingly, with opposite binding orientations. DHEAS also forms hydrogen bonds with xlσ1R, whereas progesterone interacts indirectly with the receptor through water molecules near the binding site. Binding analyses are consistent with the xlσ1R-neurosteroid complex structures. Furthermore, molecular dynamics simulations and structural data reveal a potential water entry pathway. Our results provide insight into binding of two endogenous neurosteroid ligands to σ1R.


Assuntos
Sulfato de Desidroepiandrosterona , Simulação de Dinâmica Molecular , Progesterona , Receptores sigma , Receptor Sigma-1 , Xenopus laevis , Receptores sigma/metabolismo , Receptores sigma/química , Animais , Ligantes , Sítios de Ligação , Progesterona/metabolismo , Progesterona/química , Sulfato de Desidroepiandrosterona/metabolismo , Sulfato de Desidroepiandrosterona/química , Ligação Proteica , Cristalografia por Raios X , Neuroesteroides/metabolismo , Neuroesteroides/química , Ligação de Hidrogênio , Interações Hidrofóbicas e Hidrofílicas
16.
J Chem Phys ; 161(1)2024 Jul 07.
Artigo em Inglês | MEDLINE | ID: mdl-38949285

RESUMO

The phase separation of protein and RNA mixtures underpins the assembly and regulation of numerous membraneless organelles in cells. The ubiquity of protein-RNA condensates in cellular regulatory processes is in part due to their sensitivity to RNA concentration, which affects their physical properties and stability. Recent experiments with poly-cationic peptide-RNA mixtures have revealed closed-loop phase diagrams featuring lower and upper critical solution temperatures. These diagrams indicate reentrant phase transitions shaped by biomolecular interactions and entropic forces such as solvent and ion reorganization. We employed atomistic simulations to study mixtures with various RNA-polylysine stoichiometries and temperatures to elucidate the microscopic driving forces behind reentrant phase transitions in protein-RNA mixtures. Our findings reveal an intricate interplay between hydration, ion condensation, and specific RNA-polylysine hydrogen bonding, resulting in distinct stoichiometry-dependent phase equilibria governing stabilities and structures of the condensate phase. Our simulations show that reentrant transitions are accompanied by desolvation around the phosphate groups of RNA, with increased contacts between phosphate and lysine side chains. In RNA-rich systems at lower temperatures, RNA molecules can form an extensive pi-stacking and hydrogen bond network, leading to percolation. In protein-rich systems, no such percolation-induced transitions are observed. Furthermore, we assessed the performance of three prominent water force fields-Optimal Point Charge (OPC), TIP4P-2005, and TIP4P-D-in capturing reentrant phase transitions. OPC provided a superior balance of interactions, enabling effective capture of reentrant transitions and accurate characterization of changes in solvent reorganization. This study offers atomistic insights into the nature of reentrant phase transitions using simple model peptide and nucleotide mixtures. We believe that our results are broadly applicable to larger classes of peptide-RNA mixtures exhibiting reentrant phase transitions.


Assuntos
Simulação de Dinâmica Molecular , Transição de Fase , Polilisina , RNA , Polilisina/química , RNA/química , Ligação de Hidrogênio , Poli U/química
17.
Phys Chem Chem Phys ; 26(27): 18989-18996, 2024 Jul 10.
Artigo em Inglês | MEDLINE | ID: mdl-38953374

RESUMO

Isocitrate dehydrogenase 2 (IDH2) is a homodimeric enzyme that plays an important role in energy production. A mutation R140Q in one monomer makes the enzyme tumourigenic. Enasidenib is an effective inhibitor of IDH2/R140Q. A secondary mutation Q316E leads to enasidenib resistance. This mutation was hitherto only found in trans, i.e. where one monomer has the R140Q mutation and the other carries the Q316E mutation. It is not clear if the mutation only leads to resistance when in trans or if it has been discovered in trans only by chance, since it was only reported in two patients. Using molecular dynamics (MD) simulations we show that the binding of enasidenib to IDH2 is indeed much weaker when the Q316E mutation takes place in trans not in cis, which provides a molecular explanation for the clinical finding. This is corroborated by non-covalent interaction (NCI) analysis and DFT calculations. Whereas the MD simulations show a loss of one hydrogen bond upon the resistance mutation, NCI and energy decomposition analysis (EDA) reveal that a multitude of interactions are weakened.


Assuntos
Isocitrato Desidrogenase , Simulação de Dinâmica Molecular , Mutação , Triazinas , Isocitrato Desidrogenase/genética , Isocitrato Desidrogenase/química , Isocitrato Desidrogenase/antagonistas & inibidores , Isocitrato Desidrogenase/metabolismo , Humanos , Triazinas/química , Triazinas/farmacologia , Ligação de Hidrogênio , Aminopiridinas/química , Aminopiridinas/farmacologia , Teoria da Densidade Funcional , Resistencia a Medicamentos Antineoplásicos/genética
18.
PLoS One ; 19(7): e0307501, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-39037973

RESUMO

The histone deacetylase 2 (HDAC2), an enzyme involved in gene regulation, is a potent drug target for the treatment of colon cancer. Phytocompounds having anticancer properties show the ability to interact with HDAC2 enzyme. Among the compounds, docking scores of caffeic acid (CA) and p-coumaric acid (pCA) with HDAC2 showed good binding efficacy of -5.46 kcal/mol and -5.16 kcal/mol, respectively, with small inhibition constants. The higher binding efficacy of CA compared to pCA can be credited to the presence of an extra oxygen atom in the CA molecule, which forms an additional hydrogen bond with Tyr297. The HDAC2 in complex with these molecules was found to be stable by analyzing RMSD, RMSF, Rg, and SASA values obtained through MD simulations. Furthermore, CA and pCA exhibited low MM/GBSA free energies of -16.32 ± 2.62 kcal/mol and -17.01 ± 2.87 kcal/mol, respectively. The HOMO and LUMO energy gaps, dipole moments, global reactivity descriptor values, and MEP surfaces showed the reactivity of the molecules. The favourable physicochemical and pharmacokinetic properties, along with absence of toxicity of the molecules determined using ADMET analysis, suggested both the acids to be regarded as effective drugs in the treatment of colon cancer.


Assuntos
Neoplasias do Colo , Histona Desacetilase 2 , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Neoplasias do Colo/tratamento farmacológico , Neoplasias do Colo/patologia , Humanos , Histona Desacetilase 2/antagonistas & inibidores , Histona Desacetilase 2/metabolismo , Histona Desacetilase 2/química , Inibidores de Histona Desacetilases/química , Inibidores de Histona Desacetilases/farmacologia , Ácidos Cafeicos/química , Ácidos Cafeicos/farmacologia , Propionatos/química , Propionatos/farmacologia , Ácidos Cumáricos/química , Ácidos Cumáricos/farmacologia , Ligação de Hidrogênio , Teoria da Densidade Funcional
19.
Chem Biol Drug Des ; 104(1): e14599, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-39039616

RESUMO

In this study, we synthesized 15 novel quinazoline-morpholinobenzylideneamino hybrid compounds from methyl anthranilate and we assessed their cytotoxicity via in vitro assays against A549 and BEAS-2B cell lines. Molecular docking studies were conducted to evaluate the protein-ligand interactions and inhibition mechanisms on nine different molecular targets, while molecular dynamics (MD) simulations were carried out to assess the stability of the best docked ligand-protein complexes. Additionally, ADME prediction was carried out to determine physicochemical parameters and drug likeness. According to the cytotoxicity assays, compound 1 (IC50 = 2.83 µM) was found to be the most active inhibitor against A549 cells. While the selectivity index (SI) of compound 1 is 29, the SI of the reference drugs paclitaxel and sorafenib, used in this study, are 2.40 and 4.92, respectively. Among the hybrid compounds, 1 has the best docking scores against VEGFR1 (-11.744 kcal/mol), VEGFR2 (-12.407 kcal/mol) and EGFR (-10.359 kcal/mol). During MD simulations, compound 1 consistently exhibited strong hydrogen bond interactions with the active sites of VEGFR1 and 2, and these interactions were maintained for more than 90% of the simulation time. Additionally, the RMSD and RMSF values of the ligand-protein complexes exhibited high stability at their minimum levels around 1-2 Å. In conclusion, these findings suggest that compound 1 may be a potent and selective inhibitor candidate for lung cancer treatment and inhibition of VEGFR2, especially.


Assuntos
Antineoplásicos , Neoplasias Pulmonares , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Morfolinas , Humanos , Antineoplásicos/farmacologia , Antineoplásicos/química , Antineoplásicos/síntese química , Antineoplásicos/metabolismo , Neoplasias Pulmonares/tratamento farmacológico , Neoplasias Pulmonares/metabolismo , Neoplasias Pulmonares/patologia , Morfolinas/química , Morfolinas/farmacologia , Linhagem Celular Tumoral , Receptores ErbB/metabolismo , Receptores ErbB/antagonistas & inibidores , Células A549 , Quinazolinonas/química , Quinazolinonas/farmacologia , Quinazolinonas/metabolismo , Quinazolinonas/síntese química , Receptor 2 de Fatores de Crescimento do Endotélio Vascular/antagonistas & inibidores , Receptor 2 de Fatores de Crescimento do Endotélio Vascular/metabolismo , Quinazolinas/química , Quinazolinas/farmacologia , Quinazolinas/síntese química , Quinazolinas/metabolismo , Sítios de Ligação , Ensaios de Seleção de Medicamentos Antitumorais , Ligação de Hidrogênio
20.
Food Res Int ; 189: 114561, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-38876594

RESUMO

The aim of this study was to investigate the effects of Premna microphylla turcz polysaccharide (PMP) on the rheological, gelling, and structural properties of mung bean starch (MBS) and their potential interaction mechanism. Results showed that the addition of PMP significantly improved the pasting properties, rheological properties, water holding capacity, and thermostability of MBS. The texture tests showed a decrease in hardness, gumminess and chewiness, indicating the retrogradation of MBS was inhibited. Scanning electron microscopy (SEM) suggested the MBS-PMP composite gels expressed a denser microstructure with obvious folds and tears. Moreover, the results of X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR) and interaction force tests revealed the main forces between MBS and PMP were hydrogen bonds and hydrophobic interactions to form composite gels with great gelling properties. These results facilitate the practical application of MBS and PMP, and provide some references for understanding the interaction mechanism between starch and polysaccharide.


Assuntos
Géis , Polissacarídeos , Reologia , Amido , Vigna , Amido/química , Polissacarídeos/química , Espectroscopia de Infravermelho com Transformada de Fourier , Vigna/química , Difração de Raios X , Microscopia Eletrônica de Varredura , Interações Hidrofóbicas e Hidrofílicas , Água/química , Ligação de Hidrogênio
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