Estudio computacional de las interacciones moleculares entre el timol y los residuos HIS41 y CYS145 presentes en el sitio activo de la proteasa 3CLpro

La proteína proteasa 3CLpro del SARS-CoV-2 es una enzima crucial para la replicación viral, razón por la cual se convierte en un blanco terapéutico de gran importancia. El timol (2-isopropil-5-me-tilfenol), un compuesto natural que se encuentra en el tomillo (Thymus vulgaris), exhibe potencial actividad antiviral contra la proteasa 3CLpro. En este estudio, usando acoplamiento molecular con AutoDockTools-1.5.6, se evaluaron las energías de interacción molecular entre el timol y los residuos de aminoácidos en el sitio activo de la proteína proteasa 3CLpro. Luego, con la teoría cuántica de Átomos en Moléculas (QTAIM) y la de Interacciones no covalentes (NCI) se analizaron los tipos de interacciones moleculares entre los residuos de aminoácidos identificados y el timol. Los cálculos cuánticos se llevaron con el software Orca-5.0.3, utilizando el método DFT con el funcional M06-2X y el conjunto base aug-cc-pVDZ en fase gaseosa. Los resultados de acoplamiento molecular indican que el timol se une a la proteína 3CL con una energía de interacción igual a -3,784 kcal/mol. El análisis QTAIM indica la presencia de puntos críticos de enlace entre el timol y los residuos HIS41 y CYS145. Además, se observa la formación de un enlace de hidrógeno entre el grupo OH del timol y el residuo CYS145, lo cual es corroborado por los análisis ELF (Electron Localization Function) y NCI (Non Covalent Interactions). Finalmente, el método NCI confirma la presencia de interacciones de Van der Waals con el residuo HIS41. Los resultados sugieren que el mecanismo de inhibición de la actividad de la proteína 3CLpro es controlado por interacciones moleculares tipo puente de hidrógeno e interacciones débiles.

The protease 3CLpro of the SARS-CoV-2 is a crucial enzyme for viral replication, becoming a highly important therapeutic target. Thymol (2-isopropyl-5-methyl-phenol), a naturally occurring compound found in thyme, exhibits potential antiviral activity against the 3CLpro protease. In this study, using molecular docking with AutoDockTools-1.5.6, the molecular interaction energies between thymol and amino acid residues in the active site of the protein protease 3CLpro were evaluated. Then, with the Atoms in Molecules (QTAIM) and Non-covalent Interactions (NCI) theories, the types of molecular interactions between identified amino acid residues and thymol were analyzed. Quantum calculations were carried out with the Orca-5.0.3 software using the DFT method with the M06-2X functional and the aug-cc-pVDZ basis set in the gas phase. The molecular docking results indicate that thymol is linked to the 3CL protein with an interaction energy equal to -3.784 kcal/mol. QTAIM analysis indicates the presence of critical binding sites between thymol and residues HIS41 and CYS145. In addition, the formation of a hydrogen bond between the OH group of thymol and the CYS145 residue is observed, which is corroborated by the ELF and NCI analyses. Finally, the NCI method confirms the presence of Van der Waals interactions with the HIS41 residue. The results suggest that the mechanism of inhibition of the activity of the 3CLpro protein is controlled by molecular interactions such as hydrogen bonding and weak interactions.

A protease 3CLpro do SARS-CoV-2 é uma enzima crucial para a replicação viral, tornando-se um alvo terapêutico de grande importÅncia. O timol (2-isopropil-5-me-tilfenol), um composto natural encontrado no tomilho, exibe potencial atividade antiviral contra a protease 3CLpro. Neste estudo, utilizando o docking molecular com o AutoDockTools-1.5.6, foram avaliadas as energias de interação molecular entre o timol e os residuos de aminoácidos no sítio ativo da proteína protease 3CLpro. Em seguida, com a teoria quantica de atomos em moleculas (QTAIM) e da interacões no-covalentes (NCI), foram analisados os tipos de interações moleculares entre os resíduos de aminoácidos identificados e o timol. Os cálculos quÅnticos foram realizados com o software Orca-5.0.3 usando o método DFT com o funcional M06-2X e a base aug-cc-pVDZ definida na fase gasosa. Os resultados do docking molecular indicam que o ti-mol está ligado à proteína 3CL com uma energia de interação igual a -3.784 kcal/ mol. A análise QTAIM indica a presença de sítios de ligação críticos entre o timol e os resíduos HIS41 e CYS145. Além disso, observa-se a formação de uma ponte de hidrogênio entre o grupo OH do timol e o resíduo CYS145, o que é corroborado pelas análises ELF e NCI. Finalmente, o método NCI confirma a presença das interações de Van der Waals com o resíduo HIS41. Os resultados sugerem que o mecanismo de inibição da atividade da proteína 3CLpro é controlado por interações moleculares como ligações de hidrogênio e interações fracas.

Optimization Of Formulation Of Solid Dispersion Of Furosemide By Factorial Design

Objective: The present study aimed to improve the rate of dissolution of furosemide by solid dispersion technique. Methods: Solid dispersion of furosemide was prepared by using hydrogel isolated from the seeds of Lepidium sativum as a novel carrier by the solvent evaporation method. Solid dispersion was evaluated to study the improvement in the rate of dissolution. Molecular dispersion of furosemide in the novel carrier was studied by DSC and FTIR studies. Solid dispersion was filled in capsules after stability studies and the formulation was optimized by adopting factorial design. Results: Solid dispersion of furosemide exhibited dissolution improvement from 13.54 % (plain furosemide) to 69.12% (solid dispersion) in the first 60 min. Improvement in dissolution efficiency was found to be retained after stability studies. Capsules were filled with the formulation of solid dispersion using two different grades of lactose-α lactose monohydrate and anhydrous lactose and were found stable after stabilization studies. Conclusion: The dissolution improvement of furosemide was attributed to its molecular dispersion in the novel carrier selected for this study. The recrystallization of furosemide was prevented due to intermolecular interaction between the novel carrier and furosemide. This was confirmed by FTIR. Evaluation of the dissolution data of factorial batches was analyzed by ANOVA. Analysis of the data revealed that selected levels of α lactose monohydrate and anhydrous lactose would be useful to navigate design space.

Mechanistic insights of the controlled release capacity of polar functional group in transdermal drug delivery system: the relationship of hydrogen bonding strength and controlled release capacity

Background@#Hydrogen bonding interaction was considered to play a critical role in controlling drug release from transdermal patch. However, the quantitative evaluation of hydrogen bonding strength between drug and polar functional group was rarely reported, and the relationship between hydrogen bonding strength and controlled release capacity of pressure sensitive adhesive (PSA) was not well understood. The present study shed light on this relationship.@*Methods@#Acrylate PSAs with amide group were synthesized by a free radical-initiated solution polymerization. Six drugs, , etodolac, ketoprofen, gemfibrozil, zolmitriptan, propranolol and lidocaine, were selected as model drugs. drug release and skin permeation experiments and pharmacokinetic experiment were performed. Partial correlation analysis, fourier-transform infrared spectroscopy and molecular simulation were conducted to provide molecular details of drug-PSA interactions. Mechanical test, rheology study, and modulated differential scanning calorimetry study were performed to scrutinize the free volume and molecular mobility of PSAs.@*Results@#Release rate of all six drugs from amide PSAs decreased with the increase of amide group concentrations; however, only zolmitriptan and propranolol showed decreased skin permeation rate. It was found that drug release was controlled by amide group through hydrogen bonding, and controlled release extent was positively correlated with hydrogen bonding strength.@*Conclusion@#From these results, we concluded that drugs with strong hydrogen bond forming ability and high skin permeation were suitable to use amide PSAs to regulate their release rate from patch.

Free water molecules and hydrogen bonding form the basis of variation in homeopathic potencies as revealed by vibrational spectroscopy

Using Fourier Transform Infrared spectroscopy (FTIR) we have demonstrated that homeopathic potencies of Natrum mur, Cantharis, Nux vomica and Sulphur show differences with respect to the number of free water molecules and strength of hydrogen bonding. The purpose of the present study is to confirm this phenomenon in three potencies of two more drugs Calcarea carb and Silicea. Design: The potencies used for each of the two drugs were 30cH, 200cH and 1000cH. The control was 90% ethanol as also the potentized drugs. The control, as well as the potencies, were diluted with distilled water to reduce the level of ethanol to 0.03 molar fraction in each of them. FTIR spectra of all the potentized drugs, control and sterile distilled water (reference water) were taken in the wave number region of 4000-2800 cm-1. The full width at half maximum (fwhm) of OH band was measured for each spectrum. The width was divided into two in the middle. The difference spectrum (absorbance of drug solution - absorbance of reference water) for each potency and the control was obtained after normalization of the spectrum at 3410 cm-1. One difference spectrum so obtained for a potency was subtracted from another to find out if there is a difference between two different potencies. Results: The half width half maximum (hwhm) in both the high and low-frequency sides of the OH band is far less narrow in potencies than in the control as compared to that in water. The difference spectra for different potencies show different levels of fall in intensity at the wave number region of dip at 3630 cm-1...

Effect of hydrogen on endoplasmic reticulum stress during hypoxia-reoxygenation in PC12 cells / 中华麻醉学杂志

Objective To investigate the effect of hydrogen on endoplasmic reticulum stress during hypoxiareoxygeuation(H/R)in PC12 cells.Methods PC12 cells were randomly divided into 4 groups:normal control group(group NC),positive control group(group PC),H/R group and hydrogen group(group H).In group NC.the cells were cuhnred routinely for 25 h.In group PC,the cells were cultured routinely for 1 h and then in RPM1-1640 culture medium saturated with hydrogen for 24 h.In H/R group,the cells were exposed to 1 h of hypoxia followed by 24 h of reoxygenation.In group H,the cells were exposed to 1 h of hypoxia and then reoxygenated in RPMI-1640 culture medium saturated with hydrogen for 24 h.Hypoxia-reperfusion was produced by 1 h exposure of cells to 5％ CO2 in an incubator at 37 ℃ in RPMI-1640 culture medium containing Na2S2O4 with the final concentration of 5.0 mmoI/L,followed by 24 h reoxygenation in the normal RPMI-1640 culture medium.The relative rate of cell proliferation was detected by WST-1,The concentration of MDA was determined by thiobarbituric acid method.The expression of caspase-3 was determined by immuno-histochemistry.The expression of activating transcription factor-4(ATF4)mRNA and C/EBP homologous protein(CHOP)mRNA was determined by RTPCR.Results Compared with groups NC and PC,the relative rate of cell proliferation was significantly decreased,MDA concentration was significantly increased,and the expression of caspase-3,ATF4 mRNA and CHOP mRNA was up-regulated in group H/R,and the expression of ATF4 mRNA and CHOP mRNA was up-regulated in group H(P ＜ 0.05).There was no significant difference in the relative rate of cell proliferation,MDA concentration,and the expression of caspase-3,ATF4 mRNA and CHOP mRNA between groups NC and PC(P ＞ 0.05).Compared with group H/R,the relative rate of cell proliferation was significantly increased,MDA concentration was significantly decreased,and the expression of caspase-3,ATF4 mRNA and CHOP mRNA was down-regulated in group H(P ＜ 0.05).Conclusion Hydrogen can decrease cell apoptosis and attenuate H/R injury to PC12 cells through inhibiting endoplasmic reticulum stress.

Exploring the binding affinities of p300 enzyme activators CTPB and CTB using docking method.

CREB binding protein (CBP) and E1A binding protein p300, also known as p300 are functionally related transcriptional co-activators (CoAs) and histone acetyltransferases (HATs). Some small molecules, which target HATs can activate or inhibit the p300 enzyme potently. Here, we report the binding affinities of two small molecules CTPB [N-(4-chloro- 3-trifluoromethyl-phenyl)-2-ethoxy-6-pentadecyl-benzamide] and CTB [N-(4-chloro-3-trifluoromethyl-phenyl)-2-ethoxy-benzamide] with p300 using docking method to obtain the insight of their interaction with p300. These small molecules bind to the enzyme, subsequently causing a structural change in the enzyme, which is responsible for the HAT activation. CTB exhibits higher binding affinity than CTPB, and their lowest docked energies are -7.72, -1.18 kcal/mol, respectively. In CTPB molecule, phenolic hydroxyl of Tyr1397 interacts with the non-polar atoms C(5E) and C(5F), and forms polar-non polar interactions. Similar interactions have also been observed in CTB. The residues Tyr1446 and Cys1438 interact with the non-pentadecyl atoms. Further, the docking study predicts a N-HO hydrogen bonding interaction between CTB and Leu1398, in which the HO contact distance is 2.06 Å. The long pentadecyl chain of CTPB reduces the formation of hydrogen bond with the p300. The H-bond interaction could be the key factor for the better activation of CTB.

The effect of ethylene glycol analogs on mechanical properties of moist demineralized dentin matrix / 대한치과보존학회지

OBJECTIVES: The purpose of this study is to evaluate the effect of ethylene glycol analogs on modulus of elasticity and ultimate tensile strength of moist, demineralized dentin matrix. METHODS: Dentin disks 0.5 mm thick were prepared from mid-coronal dentin of extracted, unerupted, human third molars. "I" beam and hour-glass shaped specimens were prepared from the disks, the ends protected with nail varnish and the central regions completely demineralized in 0.5M EDTA for 5 days. Ultimate tensile stress (UTS) and low strain modulus of elasticity (E) were determined with specimens immersed for 60 min in distilled water (H2O), ethylene glycol (HO-CH2-CH2-OH), 2-methoxyethanol (H3CO-CH2-CH2-OH), and 1,2-dimethoxyethane (H3CO-CH2-CH3-OCH3) prior to testing in those same media. Modulus of elasticity was measured on the same specimens in a repeated measures experimental design. The results were analyzed with a one-way ANOVA on ranks, followed by Dunn's test at alpha = 0.05. Regression analysis examined the relationship between UTS or E and hoy's solubility parameter for hydrogen bonding (delta(h)) of each solvent. RESULTS: The UTS of demineralized dentin in water, ethylene glycol, 2-methoxyethanol, and 1,2-dimethoxyethane was 24 (3), 30 (5), 37 (6), and 45 (6) MPa, x (SD) N = 10. Low strain E for the same media were 16 (13), 23 (14), 52 (24), and 62 (22) MPa. Regression analysis of UTS vs delta(h) revealed a significant (p < 0.0001, r = -0.99, R2 = 0.98) inverse, exponential relationship. A similar inverse relationship was obtained between low strain E vs delta(h) (p < 0.0005, r = -0.93, R2 = 0.86). SIGNIFICANCE: The tensile properties of demineralized dentin are dependent upon the hydrogen bonding ability of polar solvents (delta(h)). Solvents with low delta(h) values may permit new interpeptide H-bonding in collagen that increases its tensile properties. Solvents with high delta(h) values prevent the development of these new interpeptide H-bonds.

Study on the Saccharification Processes of Lignocellulose Brought about by Ultrasonic Wave / 中国生物工程杂志

Both pretreatment of lignocellulose and its saccharification process are treated with ultrasonic wave.The morphology,structure and crystal performance of the original and treated lignocellulose sample were characterized by SEM and FTIR.Moreover,the changes of raw materials caused by different pretreatment ways and the affect of saccharification rate brought about by ultrasonic wave were also studied.The result shows that the ultrasonic wave decreases the crystallinity of lignocellulose destroying the intermolecular hydrogen bonding effectively and improves the degradation rate of lignin and the saccharification rate of zymohydrolysis availably.The mechanism of activation of ultrasonic wave in zymohydrolysis process was discussed primarily.

Cyclic peptides––Small and big and their conformational aspects.

Cyclic peptides form an interesting class of compounds for study by conformational analysis, by virtue of their unique conformational features and biological properties. The small cyclic peptides having 3–6 peptide units in their ring, show a variety of conformational characteristics such as occurrence of cis peptide units, flexibility of peptide dimension and variety in hydrogen bonding. The different possible conformations of cyclic triand hexa-peptides are given and certain specific conformational features are discussed for cyclic tetra and pentapeptides. For higher cyclic peptides, the hydrogen bonding requirement for stability of the backbone of the ring, is seen to be kept to a minimum. These various features and their significance are examined and discussed in the light of energy minimization studies and analysis of available experimental data.

A guest-host approach to oligodepsipeptide structure.

In this paper we investigate the effect of main chain isosteric replacement of specific amino acid residues by α-hydroxy acids. As part of a long term program specifically protected heptaglutamates were prepared and their circular dichroism and nuclear magnetic resonance spectra in various solvents were examined. From these experiments conformational preferences were deduced. We have also prepared oligo-(γ-methyl-glutamates) replacing the amino acids at specific positions along the chain with S-lactic acid and have elucidated the effect of these main chain isosteric replacements on oligopeptide structure. Analogues of collagen also have been prepared with glycolic acid replacing specific glycine residues. We synthesized the model hexamers Ac-Ala-Gly-Pro-Ala-Gly-Pro-NHMe, Ac-Ala- Glc-Pro-Ala-Gly-Pro-NHMe, and Ac-Ala-Gly-Pro-Ala-Glc-Pro-NHMe in order to study their structural characteristics under various conditions. Preliminary nuclear magnetic resonance and circular dichroism results are presented.