Journal of Molecular Recognition最新文献

An overexpression and increase have been observed in the concentration and activity of the ubiquitin-specific protease 21 (USP21) enzyme in many cancers, necessitating the need for the development of new inhibitor drugs against the same. The current study attempts to discover one such novel potential inhibitor of USP21 by the application of various bioinformatics techniques which include molecular modeling, pharmacophore mapping, pharmacophore-based virtual screening, molecular docking, and ADMET prediction followed by molecular dynamics simulations. Following this inverted funnel-like approach, we finally ended up with one ligand–ZINC02422616 which displays a very high binding affinity toward the USP21 domain. This ligand contains all the pharmacophoric features displayed by the compounds that are potential inhibitors of the USP21 domain. Moreover, it shows a favorable pharmacokinetic, pharmacodynamic, and ADMET profile, along with strong hydrophobic interaction and hydrogen bonding with the domain. Simulation studies showed that the complex remains stable over time, with the bound protein displaying a more constrained motion in the conformational space compared to the unbound form. The ligand showed a highly favorable free energy landscape/surface, forming several energy minima's in contrast to the unbound domain in which most conformations occupied a relatively higher energy state. Moreover, the ligand also displayed a K_d of 422.8 nM and a free energy of binding ΔG of −8.6 kcal/mol, both of which indicate a very high affinity toward the target domain. This potential drug candidate can then be used as a viable treatment method for many types of cancers caused by USP21.

In this work, a series of chalcones (1a–d, 2a–d, 3a–d, 4a–d, and 5a–d) were designed and synthesized by Claisen–Schmidt condensation. Also, their chemical structures were elucidated using UV–Vis, FT IR, ¹H NMR, ¹³C NMR, MS spectral data, and elemental analyses. Subsequently, the anticholinesterase, tyrosinase, urease inhibitory activities and antioxidant activities of all chalcones were evaluated. The inhibitory potential of all chalcones in terms of IC₅₀ value was observed to range from 7.18 ± 0.43 to 29.62 ± 0.30 μM against BChE by comparing with Galantamine (IC₅₀ 46.06 ± 0.10 μM) as a reference drug. Also, compounds 2c, 3c, 4c, 4b, and 4d exhibited high anticholinesterase activity against both AChE and BChE enzymes. The tyrosinase inhibitory activity results revealed that three compounds (IC₅₀ 1.75 ± 0.83 μM for 2b, IC₅₀ 2.24 ± 0.11 μM for 3b, and IC₅₀ 1.90 ± 0.64 μM for 4b) displayed good inhibitory activity against tyrosinase compared with kojic acid (IC₅₀ 0.64 ± 0.12 μM). In addition, other different three chalcones (IC₅₀ 22.34 ± 0.25 μM for 2c, IC₅₀ 20.98 ± 0.08 μM for 3c, and IC₅₀ 18.26 ± 0.13 μM for 4c) showed excellent inhibitory activity against the urease by comparing with thiourea (IC₅₀ 23.08 ± 0.19 μM). Compounds 3c and 4c showed the best potency in all antioxidant activity tests. In light of these findings, the structure–activity relationship for compounds was also described. Furthermore, molecular modeling studies, including molecular docking, absorption, distribution, metabolism, excretion, and toxicity (ADMET), and pharmacophore analyses of compounds, gave important information about the interactions and drug-likeness properties. As a result, all chalcones exhibited suitable ADMET findings, predicting good oral bioavailability.

Visceral leishmaniasis (VL) is caused by Leishmania donovani (Ld), and most cases occur in Brazil, East Africa, and India. The treatment for VL is limited and has many adverse effects. The development of safer and more efficacious drugs is urgently needed. Drug repurposing is one of the best processes to repurpose existing drugs. Ornithine decarboxylase (ODC) is an important target against L. donovani in the polyamine biosynthesis pathway. In this study, we have modeled the 3D structure of ODC and performed high-throughput virtual screening of 8630 ZINC database ligands against Leishmania donovani ornithine decarboxylase (Ld ODC), selecting 45 ligands based on their high binding score. It is further validated through molecular docking simulation and the selection of the top two lead molecules (ceftaroline fosamil and rimegepant) for Molecular Dynamics (MD) simulation, Density functional theory (DFT), and molecular mechanics generalized born surface area (MMGBSA) analysis. The results showed that the binding affinities of ceftaroline fosamil, and rimegepant are, respectively, −10.719 and 10.159 kcal/mol. The docking complexes of the two lead compounds, ceftaroline fosamil, and rimegepant, with the target ODC, were found stable during molecular dynamics simulations. Furthermore, the analysis of MMGBSA revealed that these compounds had a high binding free energy. The DFT analysis showed that the top lead molecules were more reactive than the standard drug (pentamidine). In-silico findings demonstrated that ceftaroline fosamil, and rimegepant might be recognized as potent antagonists against ODC for the treatment of VL.

Mechanical biomarkers distinguish health conditions through quantitative mechanical measurements. The emergence and establishment of nanotechnology in the last decades have provided new tools to obtain mechanical biomarkers at the nanoscale. Mechanical measurements are reproducible, label-free, start to be applied in vivo can be high throughput, and require small samples. Mechanical protocols in clinical practice at the macro scale like palpation or blood pressure measurement are routinely used by medical doctors. Nanotechnology brought mechanical sensing to the next scale, where cells, tissues, and proteins can be probed and linked to medical conditions. Mechanical changes in cells and tissues may be detected before other markers, such as protein expression, providing an important advantage as biomarkers. In the present review, we explore the biomarker's historical evolution, describe mechanical biomarkers on various diseases and novel discoveries in the nanomechanical field for their characterization. We conclude that mechanical biomarkers are establishing novel hallmarks in diseases, in several cases for early diagnostics of diseases and discovery of drug targets in the proteins involved in the mechanical changes, while advances in instrumentation are bringing commercial products into the clinical practice. Mechanical biomarkers along with clinical testing are establishing an important niche in the market, whose demand is increasing due to the expansion of personalized medicine and unmet needs in the clinics.

Cell mechanics is a factor that determines cell growth, migration, proliferation, or differentiation, as well as trafficking inside the cytoplasm and organization of organelles. Knowledge about cell mechanics is critical to gaining insight into these biological processes. Here, we used atomic force microscopy to examine the elasticity, an important parameter of cell mechanics, of non-adherent Jurkat leukemic T-cells in both interphase and mitotic phases. We found that the elasticity of an individual cell does not significantly change at interphase. When a cell starts to divide, its elasticity increases in the transition from metaphase to telophase during normal division while the cell is stiffened right after it enters mitosis during abnormal division. At the end of the division, the cell elasticity gradually returned to the value of the mother cell. These changes may originate from the changes in cell surface tension during modulating actomyosin at the cleavage furrow, redistributing cell organelles, and constricting the contractile ring to sever mother cell to form daughters. The difference in elasticity patterns suggests that there is a discrepancy in the redistribution of the cell organelles during normal and abnormal division.

The present work determines efficiency of domestic food waste like tea waste in removing pharmaceutical waste such as ceftriaxone (CEF) from synthetic wastewater. Carbonaceous material; Tea waste activated carbon (TAC) has been employed and it showed high removal capacity of 787.5 mg/g. TAC was characterized using; XPS, XRD, SEM, FT-IR, and BET as well as it approved that the adsorbent a has high surface area of .6 m²/g. Various experimental parameters are evaluated for the removal efficiency of the synthesized adsorbent under the present study. During the adsorption study through batch experiments, it approved that the adsorption isotherm was fitted to Langmuir, while kinetically fitted to pseudo-second-order; the adsorption process was chemisorption process as the adsorption energy was 23.7 kJ mol⁻¹. From evaluation thermodynamic parameters the adsorption reaction was endothermic and spontaneous reaction. The different real samples spiked with CEF and studies the efficiency of TAC to remove it. On the other hand, investigated the regeneration efficiency of the TAC and exhibit high regeneration efficiency as it will be used after four cycles with good efficiency of about 84.2%.

The G-quadruplex planar-ligand complex is used to detect heavy metal cations such as Ag⁺, Cu²⁺, Pb²⁺, Hg²⁺, organic molecules, nucleic acids, and proteins. The interaction of the three planar porphyrins (L1), 5,10,15,20-tetrakis (1-ethyl-1-λ⁴-pyridine-4-yl) porphyrin (L2), and 5,10,15,20-tetrakis (1-methyl-1-λ⁴-pyridine-4-yl) porphyrin (L3), coming from the porphyrin family, with G-quadruplex obtained from human DNA telomeres in the presence of lithium, sodium, potassium, rubidium, cesium, magnesium, and calcium ions was studied by molecular dynamics simulation. When G-quadruplex containing divalent ions of magnesium and calcium interacts with L1, L2, and L3 ligands, the hydrogen bonds of the lower G-quadruplex sheet are more affected by ligands and the distance between guanines in the lower tetrad increases. In the case of G-quadruplex interactions containing monovalent ions with ligands, the hydrogen bond between the sheets does not follow a specific trend. For example, in the presence of lithium ions, the upper and middle sheets are more affected by ligands, while they are less affected by ligands in the presence of sodium. The binding pocket and the binding energy of the three ligands to the G-quadruplex were also obtained in the various systems. The results show that ligands make the G-quadruplex more stable through the penetration between the sheets and the interaction with the loops. Among the ligands mentioned, the interaction level of the ligand L2 is greater than the others. Our calculations are consistent with the previous experimental observations so that it can help to understand the molecular mechanism of porphyrin interaction and its derivatives with the G-quadruplex.

We have measured the elastic properties of live cells by Atomic Force Microscope (AFM) using different tip geometries commonly used in AFM studies. Soft 4-sided pyramidal probes (spring constant = 12 and 30 mN/m, radius 20 nm), 3-sided pyramidal probes (spring constant = 100 mN/m, radius 65-75 nm), flat (circular) probes (spring constant = 63 mN/m, radius 290 nm) and spherical probes (spring constant = 43 mN/m, radius 5 μm) have been used. Cells (3T3 fibroblasts) having elastic moduli around 0.5 kPa were investigated. We found that cell measured stiffness shows a systematic dependence on tip geometry: the sharper the tip, the higher the average modulus values. We hypothesize that the blunter the tip, the larger the contact area over which the mechanical response is measured or averaged. If there are small-scale stiffer areas (like actin bundles) they will be easier to pick up by a sharp probe. This effect can be seen in the wider distribution of the histograms of the measured elastic moduli on cells. Furthermore, non-linear responses of cells may be present due to the high average pressures applied by sharp probes, which would lead to an overestimation of the Young's modulus. Pressure versus contact radius simulations for the different tip geometries for a 0.5 kPa sample suggested similar average pressure for Bio-MLCTs, PFQNM and cut tips, except spherical tips that showed much lower average pressure at the same 400 nm indentation. However, real data of the cells suggested different results. Using the same indentation depth (400 nm), PFQNM and Bio-MLCTs showed similar average pressure and it decreased for cut and spherical tips. The calculated contact area at 400 nm cell indentation, using the obtained apparent Young's modulus for each tip geometry, showed the following distribution: Bio-MLCTs < PFQNM < cut << spherical. In summary, tip geometry as well as average pressure and tip-sample contact area are important parameters to take into account when measuring mechanical properties of soft samples. The larger the tip radius, the larger the contact area that will lead to a more evenly distribution of the applied pressure.

Recent interest has focused on the biosynthesis of metal nanoparticles (NPs), particularly from plants. The production of precipitate served as an early indicator of the presence in the present study's use of ZnO NPs green synthesis of these particles, which was further validated by; Fourier transform infrared spectroscopy, x-ray diffraction. Additionally, the Brunauer–Emmett–Teller was used to calculate the surface area, which came out to be 119.12 m²/g. Since the true effects of new pollutants, including medicines, on the environment and human health are not well understood, their presence in aquatic systems poses a severe hazard. For this reason, the antibiotic Ibuprofen (IBP) was absorbable to ZnO-NPs in this search. As opposed to fitting to Langmuir isothermally, the adsorption process was discovered to be pseudo-second-order kinetically, and the reaction was determined to be a chemisorption process. The process was endothermic and spontaneous, according to thermodynamic studies. Maximizing IBP removal from aqueous solution required the use of a Box–Behnken surface statistical design with four components, four levels, and response surface modeling. Solution pH, IBP concentration, duration, and dose were the four parameters that were utilized. The regeneration process, which is employed for five cycles with excellent efficiency, is the best benefit of using ZnO-NPs. Examine the elimination of pollutants from actual samples as well. However, the adsorbent is quite effective at reducing biological activity. At high concentrations of ZnO-NPs demonstrated notable antioxidant activity and Red Blood Cell (RBC) hemocompatibility and no discernible hemolysis was seen. ZnO-NPs demonstrated a notable percent suppression of α-amylase up to 53.6% at 400 μg/mL, and so displayed potential as an antidiabetic. Cyclooxygenase was suppressed by ZnO-NPs in an anti-inflammatory test (COX-1 & COX-2) up to 56.32% and 52.04% at a concentration of 400 μg/mL, respectively. Significant anti-Alzheimer potential was demonstrated by ZnO-NPs at 400 μg/mL by inhibiting Acetyl cholinesterase and Butyl cholinesterase up to 68.98 ± 1.62% and 62.36%, respectively. We concluded that guava extract is helpful for ZnO-NP reduction and capping. The bioengineered NPs could prevent Alzheimer's, diabetes, and inflammation and were biocompatible.

Human angiotensin-converting enzyme (ACE) is a well-established druggable target for the treatment of hypertension (HTN), which contains two structurally homologous but functionally distinct N- and C-domains. Selective inhibition of the C-domain primarily contributes to the antihypertensive efficiency and can be exploited as medicinal agents and functional additives for regulating blood pressure with high safety. In this study, we used a machine annealing (MA) strategy to guide the navigation of antihypertensive peptides (AHPs) in structurally interacting diversity space with the two ACE domains based on their crystal/modeled complex structures and an in-house protein-peptide affinity scoring function, aiming to optimize the peptide selectivity for C-domain over N-domain. The strategy generated a panel of theoretically designed AHP hits with a satisfactory C-over-N (C > N) selectivity profile, from which several hits were found to have a good C > N selectivity, which is roughly comparable with or even better than the BPPb, a natural C > N-selective ACE-inhibitory peptide. Structural analysis and comparison of domain-peptide noncovalent interaction patterns revealed that (i) longer peptides (>4 amino aids) generally exhibit stronger selectivity than shorter peptides (<4 amino aids), (ii) peptide sequence can be divided into two, section I (including peptide C-terminal region) and section II (including peptide middle and N-terminal regions); the former contributes to both peptide affinity (primarily) and selectivity (secondarily), while the latter is almost only responsible for peptide selectivity, and (iii) charged/polar amino acids confer to peptide selectivity relative to hydrophobic/nonpolar amino acids (that confer to peptide affinity).