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1.
Sci Rep ; 14(1): 22246, 2024 09 27.
Artigo em Inglês | MEDLINE | ID: mdl-39333193

RESUMO

Alzheimer's disease (AD) is a prevalent neurodegenerative disorder, impacting millions of individuals worldwide. Among its defining characteristics is the accumulation of senile plaques within the brain's gray matter, formed through the self-assembly of misfolded proteins contributing to the progressive symptoms of AD. This study investigates a polymorphic Aß fibril under static and oscillating electric fields using molecular dynamics simulation. Specifically, we utilized a polymorphic fibrillar complex composed of two intertwined pentamer-strands of the Aß1-40 peptide with the Osaka mutation (E22Δ), known for its toxicity and stable structure. Our findings demonstrate that a 0.3 and 0.4 V/nm electric field combined with a 0.20 GHz frequency effectively disrupts the polymorphic conformation of Aß fibrils. Furthermore, we elucidate the molecular mechanisms underlying this disruption, providing insights into the potential therapeutic use of oscillating electric fields for AD. This research offers valuable insights into novel therapeutic approaches for combating AD pathology.


Assuntos
Doença de Alzheimer , Peptídeos beta-Amiloides , Eletricidade , Simulação de Dinâmica Molecular , Mutação , Peptídeos beta-Amiloides/metabolismo , Peptídeos beta-Amiloides/genética , Peptídeos beta-Amiloides/química , Humanos , Doença de Alzheimer/genética , Doença de Alzheimer/metabolismo , Doença de Alzheimer/patologia , Fragmentos de Peptídeos/química , Fragmentos de Peptídeos/genética , Fragmentos de Peptídeos/metabolismo , Simulação por Computador , Amiloide/química , Amiloide/metabolismo
2.
J Struct Biol ; 216(3): 108109, 2024 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-38964522

RESUMO

Parkinson's disease (PD) is a category of neurodegenerative disorders (ND) that currently lack comprehensive and definitive treatment strategies. The etiology of PD can be attributed to the presence and aggregation of a protein known as α-synuclein. Researchers have observed that the application of an external electrostatic field holds the potential to induce the separation of the fibrous structures into peptides. To comprehend this phenomenon, our investigation involved simulations conducted on the α-synuclein peptides through the application of Molecular Dynamics (MD) simulation techniques under the influence of a 0.1 V/nm electric field. The results obtained from the MD simulations revealed that in the presence of external electric field, the monomer and oligomeric forms of α-synuclein are experienced significant conformational changes which could prevent them from further aggregation. However, as the number of peptide units in the model system increases, forming trimers and tetramers, the stability against the electric field also increases. This enhanced stability in larger aggregates indicates a critical threshold in α-synuclein assembly where the electric field's effectiveness in disrupting the aggregation diminishes. Therefore, our findings suggest that early diagnosis and intervention could be crucial in preventing PD progression. When α-synuclein predominantly exists in its monomeric or dimeric form, applying even a lower electric field could effectively disrupt the initial aggregation process. Inhibition of α-synuclein fibril formation at early stages might serve as a viable solution to combat PD by halting the formation of more stable and pathogenic α-synuclein fibrils.


Assuntos
Simulação de Dinâmica Molecular , Doença de Parkinson , Estabilidade Proteica , Eletricidade Estática , alfa-Sinucleína , alfa-Sinucleína/química , alfa-Sinucleína/metabolismo , Doença de Parkinson/metabolismo , Doença de Parkinson/patologia , Humanos , Agregados Proteicos , Conformação Proteica
3.
RSC Adv ; 14(21): 15085-15094, 2024 May 02.
Artigo em Inglês | MEDLINE | ID: mdl-38720970

RESUMO

Water contamination due to organic pollutants is a challenging issue around the globe, and several attempts have been made to deal with this issue. Out of which, the semiconductor-based photocatalytic process had gained much attention and proved to be an efficient, easy, and economical process for the removal of organic dyes from aqueous solutions. For this purpose, the iron oxide-zirconium dioxide nanocomposite (Fe2O3-ZrO2 NC) was prepared via a simple mechanochemical process using a mortar and pestle, followed by a calcination process at 300, 600, and 900 °C. Different physicochemical analyses were carried out in order to investigate the successful synthesis of Fe2O3-ZrO2 NC and the effect of temperature on the crystallinity, surface area, pore size, phase composition, sample morphology, and particle/crystallite size. The Fe2O3-ZrO2 NCs were subjected to a photocatalytic test under solar light irradiation against fluorescein dye in an aqueous medium, and the photocatalytic performance was examined under the influence of calcination temperatures, pH, catalyst dose, and initial concentration. The stability of the Fe2O3-ZrO2 NCs was also checked by recycling them for five reuse cycles.

4.
PLoS One ; 19(2): e0296916, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38335221

RESUMO

Equilibrium molecular dynamics (EMD) simulations have been performed to investigate the structural analysis and thermal conductivity (λ) of semiconducting (8,0) and metallic (12,0) zigzag single-walled carbon nanotubes (SWCNTs) for varying ±Î³(%) strains. For the first time, the present outcomes provide valuable insights into the relationship between the structural properties of zigzag SWCNTs and corresponding thermal behavior, which is essential for the development of high-performance nanocomposites. The radial distribution function (RDF) has been employed to assess the buckling and deformation understandings of the (8,0) and (12,0) SWCNTs for a wide range of temperature T(K) and varying ±Î³(%) strains. The visualization of SWCNTs shows that the earlier buckling and deformation processes are observed for semiconducting SWCNTs as compared to metallic SWCNTs for high T(K) and it also evident through an abrupt increase in RDF peaks. The RDF and visualization analyses demonstrate that the (8,0) SWCNTs can more tunable under compressive than tensile strains, however, the (12,0) zigzag SWCNTs indicate an opposite trend and may tolerate more tensile than compressive strains. Investigations show that the tunable domain of ±Î³(%) strains decreases from (-10%≤ γ ≤+19%) to (-5%≤ γ ≤+10%) for (8,0) SWCNTs and the buckling process shifts to lower ±Î³(%) for (12,0) SWCNTs with increasing T(K). For intermediate-high T(K), the λ(T) of (12,0) SWCNTs is high but the (8,0) SWCNTs show certainly high λ(T) for low T(K). The present λ(T, ±Î³) data are in reasonable agreement with parts of previous NEMD, GK-HNEMD data and experimental investigations with simulation results generally under predicting the λ(T, ±Î³) by the ∼1% to ∼20%, regardless of the ±Î³(%) strains, depending on T(K). Our simulation data significantly expand the strain range to -10% ≤ γ ≤ +19% for both zigzag SWCNTs, depending on temperature T(K). This extension of the range aims to establish a tunable regime and delve into the intrinsic characteristics of zigzag SWCNTs, building upon previous work.


Assuntos
Simulação de Dinâmica Molecular , Nanotubos de Carbono , Nanotubos de Carbono/química
5.
J Chem Theory Comput ; 20(3): 1263-1273, 2024 Feb 13.
Artigo em Inglês | MEDLINE | ID: mdl-38227434

RESUMO

The borohydride ion, BH4-, is an essential reducing agent in many technological processes, yet its full understanding has been elusive, because of at least two significant challenges. One challenge arises from its marginal stability in aqueous solutions outside of basic pH conditions, which considerably limits the experimental thermodynamic data. The other challenge comes from its unique and atypical hydration shell, stemming from the negative excess charge on its hydrogen atoms, which complicates the accurate modeling in classical atomistic simulations. In this study, we combine experimental and computer simulation techniques to devise a classical force field for NaBH4 and deepen our understanding of its characteristics. We report the first measurement of the ion's activity coefficient and extrapolate it to neutral pH conditions. Given the difficulties in directly measuring its solvation free energies, owing to its instability, we resort to quantum chemistry calculations. This combined strategy allows us to derive a set of nonpolarizable force-field parameters for the borohydride ion for classical molecular dynamics simulations. The derived force field simultaneously captures the solvation free energy, the hydration structure, as well as the activity coefficient of NaBH4 salt across a broad concentration range. The obtained insights into the hydration shell of the BH4- ion are crucial for accurately modeling and understanding its interactions with other molecules, ions, materials, and interfaces.

6.
Arch Biochem Biophys ; 751: 109835, 2024 01.
Artigo em Inglês | MEDLINE | ID: mdl-38000492

RESUMO

The overexpression of voltage dependent anion channels (VDACs), particularly VDAC1, in cancer cells compared to normal cells, plays a crucial role in cancer cell metabolism, apoptosis regulation, and energy homeostasis. In this study, we used molecular dynamics (MD) simulations to investigate the effect of a low level of VDAC1 oxidation (induced e.g., by cold atmospheric plasma (CAP)) on the pyruvate (Pyr) uptake by VDAC1. Inhibiting Pyr uptake through VDAC1 can suppress cancer cell proliferation. Our primary target was to study the translocation of Pyr across the native and oxidized forms of hVDAC1, the human VDAC1. Specifically, we employed MD simulations to analyze the hVDAC1 structure by modifying certain cysteine residues to cysteic acids and methionine residues to methionine sulfoxides, which allowed us to investigate the effect of oxidation. Our results showed that the free energy barrier for Pyr translocation through the native and oxidized channel was approximately 4.3 ± 0.7 kJ mol-1 and 10.8 ± 1.8 kJ mol-1, respectively. An increase in barrier results in a decrease in rate of Pyr permeation through the oxidized channel. Thus, our results indicate that low levels of CAP oxidation reduce Pyr translocation, resulting in decreased cancer cell proliferation. Therefore, low levels of oxidation are likely sufficient to treat cancer cells given the inhibition of Pyr uptake.


Assuntos
Neoplasias , Ácido Pirúvico , Humanos , Canal de Ânion 1 Dependente de Voltagem/química , Canal de Ânion 1 Dependente de Voltagem/metabolismo , Apoptose , Cisteína/química , Oxirredução , Metionina/metabolismo
7.
Phys Biol ; 21(1)2023 Nov 23.
Artigo em Inglês | MEDLINE | ID: mdl-37963412

RESUMO

Acetylcholinesterase (AChE) is crucial for the breakdown of acetylcholine to acetate and choline, while the inhibition of AChE by anatoxin-a (ATX-a) results in severe health complications. This study explores the structural characteristics of ATX-a and its interactions with AChE, comparing to the reference molecule atropine for binding mechanisms. Molecular docking simulations reveal strong binding affinity of both ATX-a and atropine to AChE, interacting effectively with specific amino acids in the binding site as potential inhibitors. Quantitative assessment using the MM-PBSA method demonstrates a significantly negative binding free energy of -81.659 kJ mol-1for ATX-a, indicating robust binding, while atropine exhibits a stronger binding affinity with a free energy of -127.565 kJ mol-1. Umbrella sampling calculates the ΔGbindvalues to evaluate binding free energies, showing a favorable ΔGbindof -36.432 kJ mol-1for ATX-a and a slightly lower value of -30.12 kJ mol-1for atropine. This study reveals the dual functionality of ATX-a, acting as both a nicotinic acetylcholine receptor agonist and an AChE inhibitor. Remarkably, stable complexes form between ATX-a and atropine with AChE at its active site, exhibiting remarkable binding free energies. These findings provide valuable insights into the potential use of ATX-a and atropine as promising candidates for modulating AChE activity.


Assuntos
Acetilcolinesterase , Atropina , Acetilcolinesterase/química , Acetilcolinesterase/metabolismo , Simulação de Acoplamento Molecular , Ligação Proteica , Sítios de Ligação , Simulação de Dinâmica Molecular
8.
Nanomaterials (Basel) ; 13(18)2023 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-37764588

RESUMO

2H MoTe2 (molybdenum ditelluride) has generated significant interest because of its superconducting, nonvolatile memory, and semiconducting of new materials, and it has a large range of electrical properties. The combination of transition metal dichalcogenides (TMDCs) and two dimensional (2D) materials like hexagonal boron nitride (h-BN) in lateral heterostructures offers a unique platform for designing and engineering novel electronic devices. We report the fabrication of highly conductive interfaces in crystalline ionic liquid-gated (ILG) field-effect transistors (FETs) consisting of a few layers of MoTe2/h-BN heterojunctions. In our initial exploration of tellurium-based semiconducting TMDs, we directed our attention to MoTe2 crystals with thicknesses exceeding 12 nm. Our primary focus centered on investigating the transport characteristics and quantitatively assessing the surface interface heterostructure. Our transconductance (gm) measurements indicate that the very efficient carrier modulation with an ILG FET is two times larger than standard back gating, and it demonstrates unipolarity of the device. The ILG FET exhibited highly unipolar p-type behavior with a high on/off ratio, and it significantly increased the mobility in MoTe2/h-BN heterochannels, achieving improvement as one of the highest recorded mobility increments. Specifically, we observed hole and electron mobility values ranging from 345 cm2 V-1 s-1 to 285 cm2 V-1 s-1 at 80 K. We predict that our ability to observe the intrinsic, heterointerface conduction in the channels was due to a drastic reduction of the Schottky barriers, and electrostatic gating is suggested as a method for controlling the phase transitions in the few layers of TMDC FETs. Moreover, the simultaneous structural phase transitions throughout the sample, achieved through electrostatic doping control, presents new opportunities for developing phase change devices using atomically thin membranes.

9.
Biomolecules ; 13(7)2023 06 27.
Artigo em Inglês | MEDLINE | ID: mdl-37509079

RESUMO

The potential of cold atmospheric plasma (CAP) in biomedical applications has received significant interest, due to its ability to generate reactive oxygen and nitrogen species (RONS). Upon exposure to living cells, CAP triggers alterations in various cellular components, such as the cell membrane. However, the permeation of RONS across nitrated and oxidized membranes remains understudied. To address this gap, we conducted molecular dynamics simulations, to investigate the permeation capabilities of RONS across modified cell membranes. This computational study investigated the translocation processes of less hydrophilic and hydrophilic RONS across the phospholipid bilayer (PLB), with various degrees of oxidation and nitration, and elucidated the impact of RONS on PLB permeability. The simulation results showed that less hydrophilic species, i.e., NO, NO2, N2O4, and O3, have a higher penetration ability through nitro-oxidized PLB compared to hydrophilic RONS, i.e., HNO3, s-cis-HONO, s-trans-HONO, H2O2, HO2, and OH. In particular, nitro-oxidation of PLB, induced by, e.g., cold atmospheric plasma, has minimal impact on the penetration of free energy barriers of less hydrophilic species, while it lowers these barriers for hydrophilic RONS, thereby enhancing their translocation across nitro-oxidized PLB. This research contributes to a better understanding of the translocation abilities of RONS in the field of plasma biomedical applications and highlights the need for further analysis of their role in intracellular signaling pathways.


Assuntos
Peróxido de Hidrogênio , Oxigênio , Peróxido de Hidrogênio/metabolismo , Espécies Reativas de Oxigênio/metabolismo , Membrana Celular/metabolismo , Oxigênio/metabolismo , Simulação de Dinâmica Molecular , Espécies Reativas de Nitrogênio/metabolismo , Fosfolipídeos/metabolismo
10.
Int J Mol Sci ; 24(7)2023 Mar 28.
Artigo em Inglês | MEDLINE | ID: mdl-37047286

RESUMO

The self-association of amylogenic proteins to the fibril form is considered a pivotal factor in the pathogenesis of neurodegenerative diseases, including Parkinson's disease (PD). PD causes unintended or uncontrollable movements in its common symptoms. α-synuclein is the major cause of PD development and thus has been the main target of numerous studies to suppress and sequester its expression or effectively degrade it. Nonetheless, to date, there are no efficient and proven ways to prevent pathological protein aggregation. Recent investigations proposed applying an external electric field to interrupt the fibrils. This method is a non-invasive approach that has a certain benefit over others. We performed molecular dynamics (MD) simulations by applying an electric field on highly toxic fibrils of α-synuclein to gain a molecular-level insight into fibril disruption mechanisms. The results revealed that the applied external electric field induces substantial changes in the conformation of the α-synuclein fibrils. Furthermore, we show the threshold value for electric field strength required to completely disrupt the α-synuclein fibrils by opening the hydrophobic core of the fibril. Thus, our findings might serve as a valuable foundation to better understand molecular-level mechanisms of the α-synuclein fibrils disaggregation process under an applied external electric field.


Assuntos
Doença de Parkinson , alfa-Sinucleína , Humanos , alfa-Sinucleína/metabolismo , Simulação de Dinâmica Molecular , Doença de Parkinson/metabolismo , Agregação Patológica de Proteínas/complicações , Amiloide/metabolismo
11.
Biomolecules ; 13(2)2023 02 07.
Artigo em Inglês | MEDLINE | ID: mdl-36830684

RESUMO

Although modern medicine is advancing at an unprecedented rate, basic challenges in cancer treatment and drug resistance remain. Exploiting natural-product-based drugs is a strategy that has been proven over time to provide diverse and efficient approaches in patient care during treatment and post-treatment periods of various diseases, including cancer. Escin-a plant-derived triterpenoid saponin-is one example of natural products with a broad therapeutic scope. Initially, escin was proven to manifest potent anti-inflammatory and anti-oedematous effects. However, in the last two decades, other novel activities of escin relevant to cancer treatment have been reported. Recent studies demonstrated escin's efficacy in compositions with other approved drugs to accomplish synergy and increased bioavailability to broaden their apoptotic, anti-metastasis, and anti-angiogenetic effects. Here, we comprehensively discuss and present an overview of escin's chemistry and bioavailability, and highlight its biological activities against various cancer types. We conclude the review by presenting possible future directions of research involving escin for medical and pharmaceutical applications as well as for basic research.


Assuntos
Escina , Neoplasias , Humanos , Escina/química , Escina/uso terapêutico , Neoplasias/tratamento farmacológico , Extratos Vegetais
12.
Heliyon ; 9(1): e12576, 2023 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-36699268

RESUMO

Metallic nanowires (NWs) and their different compounds display incredible prospects for their use in various applications including media storage, sensor and solar cell devices along with the biological drug delivery systems. In this research work, the metallic NWs like nickel nanowires (Ni-NWs) are synthesized successfully by employing electrodeposition process. Anodic aluminum oxide (AAO) templates are employed as a platform with copper metal coating which acts as an active cathode. The synthesized Ni-NWs are examined through various characterization techniques including X-ray diffraction (XRD), scanning electron microscope (SEM) and vibrating sample magnetometer (VSM) to study the crystal structure, surface morphology and magnetic properties, respectively. The XRD analysis shows the development of various diffraction planes like Ni (111), Ni (200), Ni (220) which confirms the formation of polycrystalline nickel NWs. The SEM analysis reveals that the range of diameter and length of nickel NWs are found to be ∼160 to 200 and ∼4 to 11 micron respectively showing high aspect ratio (ranged from ∼200 to 300). The ferromagnetic behavior of Ni-NWs is confirmed by the hysteresis loop carried out for parallel and perpendicular configurations having Hc = 100 and 206 Oe, respectively. The obtained results suggest that the synthesized Ni- NWs may be used for high-density media storage devices.

13.
Biomed Pharmacother ; 160: 114320, 2023 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-36716660

RESUMO

Glioblastoma Multiforme (GBM) is known to be by far the most aggressive brain tumor to affect adults. The median survival rate of GBM patient's is < 15 months, while the GBM cells aggressively develop resistance to chemo- and radiotherapy with their self-renewal capacity which suggests the pressing need to develop novel preventative measures. We have recently proved that GPR17 -an orphan G protein-coupled receptor- is highly expressed on the GBM cell surface and it has a vital role to play in the disease progression. Despite the progress made on GBM downregulation, there still remain difficulties in developing a promising modulator for GPR17, till date. Here, we have performed robust virtual screening combined with biased-force pulling molecular dynamic (MD) simulations to predict high-affinity GPR17 modulators followed by experimental validation. Initially, the database containing 1379 FDA-approved drugs were screened against the orthosteric binding pocket of the GPR17. The external bias-potentials were then applied to the screened hits during the MD simulations which enabled to predict a spectrum of rupture peak force values that were used to select four approved drugs -ZINC000003792417 (Sacubitril), ZINC000014210457 (Victrelis), ZINC000001536109 (Pralatrexate) and ZINC000003925861 (Vorapaxar)- as top hits. The hits selected turns out to demonstrate unique dissociation pathways, interaction pattern, and change in polar network over time. Subsequently the selected hits with GPR17 were measured by inhibiting the forskolin-stimulated cAMP accumulation in GBM cell lines, LN229 and SNB19. The ex vivo validations shows that Sacubitril drug can act as a full agonist, while Vorapaxar functions as a partial agonist for GPR17. The pEC50 of Sacubitril was identified as 4.841 and 4.661 for LN229 and SNB19, respectively. Small interference of the RNA (siRNA)- silenced the GPR17 to further validate the targeted binding of Sacubitril with GPR17. In the current investigation, we have identified new repurposable GPR17 specific drugs which are likely to increase the opportunity to treat orphan deadly diseases.


Assuntos
Lactonas , Receptores Acoplados a Proteínas G , Humanos , Receptores Acoplados a Proteínas G/metabolismo , Piridinas
14.
Int J Mol Sci ; 23(11)2022 Jun 06.
Artigo em Inglês | MEDLINE | ID: mdl-35683009

RESUMO

Due to their potential benefits, cold atmospheric plasmas (CAPs), as biotechnological tools, have been used for various purposes, especially in medical and agricultural applications. The main effect of CAP is associated with reactive oxygen and nitrogen species (RONS). In order to deliver these RONS to the target, direct or indirect treatment approaches have been employed. The indirect method is put into practice via plasma-activated water (PAW). Despite many studies being available in the field, the permeation mechanisms of RONS into water at the molecular level still remain elusive. Here, we performed molecular dynamics simulations to study the permeation of RONS from vacuum into the water interface and bulk. The calculated free energy profiles unravel the most favourable accumulation positions of RONS. Our results, therefore, provide fundamental insights into PAW and RONS chemistry to increase the efficiency of PAW in biological applications.


Assuntos
Gases em Plasma , Água , Gases em Plasma/química , Espécies Reativas de Nitrogênio/química , Espécies Reativas de Oxigênio/química , Vácuo , Água/química
15.
Pharmaceutics ; 13(7)2021 Jun 25.
Artigo em Inglês | MEDLINE | ID: mdl-34201915

RESUMO

Iodine, being an intrinsic part of thyroid hormones, is a vital microelement required for normal growth and development, particularly in children. Inadequate daily intake of iodine causes iodine deficiency, which is responsible for several health disorders, such as cretinism and goiters. Therefore, the development of new drugs and/or food supplements for iodine deficiency is crucial. We synthesized an iodine/ß-cyclodextrin complex based on a host-guest model, and in this paper, we outline the development of a new quantitative analysis method. We suggest a robust and reliable high-performance liquid chromatography method to determine the total amount of iodine species in the complex. Moreover, we performed validation of our method. The results of validation presented here show the reliability, accuracy and high precision of the method. Furthermore, for the first time, we show results of in vivo studies for the thyroid-stimulating activity of the iodine/ß-cyclodextrin complex. Our findings indicate that the thyroid-stimulating activity of iodine/ß-cyclodextrin is comparable to that of potassium iodide, which is the main active pharmaceutical substance of conventional drugs for iodine deficiency.

16.
Molecules ; 26(13)2021 Jun 22.
Artigo em Inglês | MEDLINE | ID: mdl-34206308

RESUMO

Horse chestnut (Aesculus hippocastanum L.)-derived drugs have shown their potential in biomedical applications. The seed of A. hippocastanum contains various kinds of chemical compounds including phenolics, flavonoids, coumarins, and triterpene saponins. Here, we investigated the chemical components in A. hippocastanum L. grown in Uzbekistan, which has not yet been studied in detail. We identified 30 kinds of triterpene saponins in an extract of A. hippocastanum L. Classifying extracted saponins into eight fractions, we next studied the hypoglycemic and the anti-inflammatory activities of escin and its derivatives through in vivo experiments. We came by data indicating the highest (SF-1 and SF-2) and the lowest (SF-5 and SF-8) antidiabetic and anti-inflammatory effects of those eight fractions. These results imply the prospective use of A. hippocastanum L. grown in Uzbekistan in the production of pharmaceutical drugs to treat diabetes and inflammation.


Assuntos
Aesculus/química , Anti-Inflamatórios , Glicosídeos , Hipoglicemiantes , Triterpenos , Animais , Anti-Inflamatórios/química , Anti-Inflamatórios/isolamento & purificação , Anti-Inflamatórios/farmacologia , Feminino , Glicosídeos/química , Glicosídeos/isolamento & purificação , Glicosídeos/farmacologia , Hipoglicemiantes/química , Hipoglicemiantes/isolamento & purificação , Hipoglicemiantes/farmacologia , Masculino , Ratos , Ratos Wistar , Triterpenos/química , Triterpenos/isolamento & purificação , Triterpenos/farmacologia , Uzbequistão
17.
Redox Biol ; 43: 101968, 2021 07.
Artigo em Inglês | MEDLINE | ID: mdl-33895486

RESUMO

Multiple cancer therapies nowadays rely on oxidative stress to damage cancer cells. Here we investigated the biological and molecular effect of oxidative stress on the interaction between CD44 and hyaluronan (HA), as interrupting their binding can hinder cancer progression. Our experiments demonstrated that the oxidation of HA decreased its recognition by CD44, which was further enhanced when both CD44 and HA were oxidized. The reduction of CD44-HA binding negatively affected the proliferative state of cancer cells. Our multi-level atomistic simulations revealed that the binding free energy of HA to CD44 decreased upon oxidation. The effect of HA and CD44 oxidation on CD44-HA binding was similar, but when both HA and CD44 were oxidized, the effect was much larger, in agreement with our experiments. Hence, our experiments and computations support our hypothesis on the role of oxidation in the disturbance of CD44-HA interaction, which can lead to the inhibition of proliferative signaling pathways inside the tumor cell to induce cell death.


Assuntos
Ácido Hialurônico , Neoplasias , Receptores de Hialuronatos , Estresse Oxidativo , Transdução de Sinais
18.
Cancers (Basel) ; 13(3)2021 Feb 02.
Artigo em Inglês | MEDLINE | ID: mdl-33540720

RESUMO

Non-thermal plasma (NTP) therapy has been emerging as a promising cancer treatment strategy, and recently, its ability to locally induce immunogenic cancer cell death is being unraveled. We hypothesized that the chemical species produced by NTP reduce immunosuppressive surface proteins and checkpoints that are overexpressed on cancerous cells. Here, 3D in vitro tumor models, an in vivo mouse model, and molecular dynamics simulations are used to investigate the effect of NTP on CD47, a key innate immune checkpoint. CD47 is immediately modulated after NTP treatment and simulations reveal the potential oxidized salt-bridges responsible for conformational changes. Umbrella sampling simulations of CD47 with its receptor, signal-regulatory protein alpha (SIRPα), demonstrate that the induced-conformational changes reduce its binding affinity. Taken together, this work provides new insight into fundamental, chemical NTP-cancer cell interaction mechanisms and a previously overlooked advantage of present NTP cancer therapy: reducing immunosuppressive signals on the surface of cancer cells.

19.
Biomolecules ; 10(8)2020 07 28.
Artigo em Inglês | MEDLINE | ID: mdl-32731448

RESUMO

Mcl1 is a primary member of the Bcl-2 family-anti-apoptotic proteins (AAP)-that is overexpressed in several cancer pathologies. The apoptotic regulation is mediated through the binding of pro-apoptotic peptides (PAPs) (e.g., Bak and Bid) at the canonical hydrophobic binding groove (CBG) of Mcl1. Although all PAPs form amphipathic α-helices, their amino acid sequences vary to different degree. This sequence variation exhibits a central role in the binding partner selectivity towards different AAPs. Thus, constructing a novel peptide or small organic molecule with the ability to mimic the natural regulatory process of PAP is essential to inhibit various AAPs. Previously reported experimental binding free energies (BFEs) were utilized in the current investigation aimed to understand the mechanistic basis of different PAPs targeted to mMcl1. Molecular dynamics (MD) simulations used to estimate BFEs between mMcl1-PAP complexes using Molecular Mechanics-Generalized Born Solvent Accessible (MMGBSA) approach with multiple parameters. Predicted BFE values showed an excellent agreement with the experiment (R2 = 0.92). The van-der Waals (ΔGvdw) and electrostatic (ΔGele) energy terms found to be the main energy components that drive heterodimerization of mMcl1-PAP complexes. Finally, the dynamic network analysis predicted the allosteric signal transmission pathway involves more favorable energy contributing residues. In total, the results obtained from the current investigation may provide valuable insights for the synthesis of a novel peptide or small organic inhibitor targeting Mcl1.


Assuntos
Regulação Alostérica/efeitos dos fármacos , Desenho de Fármacos , Proteína de Sequência 1 de Leucemia de Células Mieloides/antagonistas & inibidores , Peptídeos/química , Peptídeos/farmacologia , Sequência de Aminoácidos , Animais , Sítios de Ligação , Humanos , Simulação de Dinâmica Molecular , Proteína de Sequência 1 de Leucemia de Células Mieloides/química , Proteína de Sequência 1 de Leucemia de Células Mieloides/metabolismo , Termodinâmica
20.
Int J Biol Macromol ; 158: 364-374, 2020 May 03.
Artigo em Inglês | MEDLINE | ID: mdl-32376253

RESUMO

Mcl1 is an important anti-apoptotic member of the Bcl2 family proteins that are upregulated in several cancer malignancies. The canonical binding groove (CBG) located at the surface of Mcl1 exhibits a critical role in binding partners selectively via the BH3-domain of pro-apoptotic Bcl2 family members that trigger the downregulation of Mcl1 function. There are several crystal structures of point-mutated pro-apoptotic Bim peptides in complex with Mcl1. However, the mechanistic effects of such point-mutations towards peptide binding and complex stability still remain unexplored. Here, the effects of the reported point mutations in Bim peptides and their binding mechanisms to Mcl1 were computationally evaluated using atomistic-level steered molecular dynamics (SMD) simulations. A range of external-forces and constant-velocities were applied to the Bim peptides to uncover the mechanistic basis of peptide dissociation from the CBG of Mcl1. Although the peptides showed similarities in their dissociation pathways, the peak rupture forces varied significantly. According to simulations results, the disruption of the conserved polar contacts at the complex interface causes a sequential release of the peptides from the CBG of Mcl1. Overall, the results obtained from the current study may provide valuable insights for the development of novel anti-cancer peptide-inhibitors that can downregulate Mcl1's function.

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