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91.
Son Tung Ngo Trung Hai Nguyen Nguyen Thanh Tung Pham Cam Nam Khanh B. Vu Van V. Vu 《Journal of computational chemistry》2020,41(7):611-618
Determination of the ligand-binding affinity is an extremely interesting problem. Normally, the free energy perturbation (FEP) method provides an appropriate result. However, it is of great interest to improve the accuracy and precision of this method. In this context, temperature replica exchange molecular dynamics implementation of the FEP computational approach, which we call replica exchange free energy perturbation (REP) was proposed. In particular, during REP simulations, the system can easily escape from being trapped in local minima by exchanging configurations with high temperatures, resulting in significant improvement in the accuracy and precision of protein–ligand binding affinity calculations. The distribution of the decoupling free energy was enlarged, and its mean values were decreased. This results in changes in the magnitude of the calculated binding free energies as well as in alteration in the binding mechanism. Moreover, the REP correlation coefficient with respect to experiment ( RREP = 0.85 ± 0.15 ) is significantly boosted in comparison with the FEP one ( RFEP = 0.64 ± 0.30 ). Furthermore, the root-mean-square error (RMSE) of REP is also smaller than FEP, RMSEREP = 4.28 ± 0.69 versus RMSEFEP = 5.80 ± 1.11 kcal/mol, respectively. © 2019 Wiley Periodicals, Inc. 相似文献
92.
Yuli Zhang Hieu M. Pham Jose G. Munguia-Lopez Joseph M. Kinsella Simon D. Tran 《Molecules (Basel, Switzerland)》2020,25(23)
Hydrogels have been used for a variety of biomedical applications; in tissue engineering, they are commonly used as scaffolds to cultivate cells in a three-dimensional (3D) environment allowing the formation of organoids or cellular spheroids. Egg white-alginate (EWA) is a novel hydrogel which combines the advantages of both egg white and alginate; the egg white material provides extracellular matrix (ECM)-like proteins that can mimic the ECM microenvironment, while alginate can be tuned mechanically through its ionic crosslinking property to modify the scaffold’s porosity, strength, and stiffness. In this study, a frozen calcium chloride (CaCl2) disk technique to homogenously crosslink alginate and egg white hydrogel is presented for 2.5D culture of human salivary cells. Different EWA formulations were prepared and biologically evaluated as a spheroid-like structure platform. Although all five EWA hydrogels showed biocompatibility, the EWA with 1.5% alginate presented the highest cell viability, while EWA with 3% alginate promoted the formation of larger size salivary spheroid-like structures. Our EWA hydrogel has the potential to be an alternative 3D culture scaffold that can be used for studies on drug-screening, cell migration, or as an in vitro disease model. In addition, EWA can be used as a potential source for cell transplantation (i.e., using this platform as an ex vivo environment for cell expansion). The low cost of producing EWA is an added advantage. 相似文献
93.
Samuel W. Foster Xiaofeng Xie Michelle Pham Paul A. Peaden Leena M. Patil Luke T. Tolley Paul B. Farnsworth H. Dennis Tolley Milton L. Lee James P. Grinias 《Journal of separation science》2020,43(9-10):1623-1627
A newly developed portable capillary liquid chromatograph was investigated for the separation of various pharmaceutical and illicit drug compounds. The system consists of two high‐pressure syringe pumps capable of delivering capillary‐scale flow rates at pressures up to 10 000 psi. Capillary liquid chromatography columns packed with sub‐2 μm particles are housed in cartridges that can be inserted into the system and easily connected through high‐pressure fluidic contact points by simply applying a specific, predetermined torque rather than using standard fittings and less precise sealing protocols. Several over‐the‐counter analgesic drug separations are demonstrated, along with a simple online measurement of tablet dissolution. Twenty illicit drug compounds were also separated across six targeted drug panels. The results described in this study demonstrate the capability of this compact liquid chromatography instrument to address several important drug‐related applications while simplifying system operation, and greatly reducing solvent usage and waste generation essential for onsite analysis. 相似文献
94.
We report design, synthesis and evaluation of a series of naphthalenediimides (NDIs) that are bridged with short peptides. Reminiscent of peptide stapling technologies, the macrocycles are conveniently accessible by a chromogenic nucleophilic aromatic substitution of two bromides in the NDI core with two thiols from cysteine sidechains. The dimension of core‐bridged NDIs matches that of one turn of an α helix. NDI‐stapled peptides exist as two, often separable atropisomers. Introduction of tertiary amine bases in amino‐acid sidechains above the π‐acidic NDI surface affords operational anion‐π catalysts. According to an enolate chemistry benchmark reaction, anion‐π catalysis next to peptides occurs with record chemoselectivity but weak enantioselectivity. Catalytic activity drops with increasing distance of the amine base to the NDI surface, looser homocysteine bridges, mismatched, shortened and elongated α‐helix turns, and acyclic peptide controls. Elongation of isolated turns into short α helices significantly increases activity. This increase is consistent with remote control of anion‐π catalysis from the α‐helix macrodipole. 相似文献
95.
96.
Yukiko Yasuoka Yuichiro Izumi Takashi Fukuyama Haruki Omiya Truyen D. Pham Hideki Inoue Tomomi Oshima Taiga Yamazaki Takayuki Uematsu Noritada Kobayashi Yoshitaka Shimada Yasushi Nagaba Tetsuro Yamashita Masashi Mukoyama Yuichi Sato Susan M. Wall Jeff M. Sands Noriko Takahashi Katsumasa Kawahara Hiroshi Nonoguchi 《Molecules (Basel, Switzerland)》2022,27(3)
Anemia is a major complication of chronic renal failure. To treat this anemia, prolylhydroxylase domain enzyme (PHD) inhibitors as well as erythropoiesis-stimulating agents (ESAs) have been used. Although PHD inhibitors rapidly stimulate erythropoietin (Epo) production, the precise sites of Epo production following the administration of these drugs have not been identified. We developed a novel method for the detection of the Epo protein that employs deglycosylation-coupled Western blotting. With protein deglycosylation, tissue Epo contents can be quantified over an extremely wide range. Using this method, we examined the effects of the PHD inhibitor, Roxadustat (ROX), and severe hypoxia on Epo production in various tissues in rats. We observed that ROX increased Epo mRNA expression in both the kidneys and liver. However, Epo protein was detected in the kidneys but not in the liver. Epo protein was also detected in the salivary glands, spleen, epididymis and ovaries. However, both PHD inhibitors (ROX) and severe hypoxia increased the Epo protein abundance only in the kidneys. These data show that, while Epo is produced in many tissues, PHD inhibitors as well as severe hypoxia regulate Epo production only in the kidneys. 相似文献
97.
Nonlinear Dynamics - In this paper, a detailed review on the dynamics of axially moving systems is presented. Over the past 60 years, vibration control of axially moving systems has attracted... 相似文献
98.
In this work,the entropy functions of ideal quantum gases in a three-dimensional harmonic trap are analytically calculated using temperature as an explicit variable.Afterward,the applicability of the analytical formulas is validated by comparison with the numerical calculation.The results illustrate that the obtained functions could be applied for the whole temperature regime with a maximum relative deviation of less than 7.5%in the vicinity of the critical temperature Tcin the case of Bose gases.Meanwhile,for Fermi gases,although the analytical formula fits well at very low-and high-temperature regimes,it cannot be applied at temperature in the range[0.3-0.5]T_F,where T_F is the Fermi temperature.In addition,the consistency between our formulas and classical ones at significantly high temperatures is also discussed. 相似文献
99.
Pham Y. Yu Y. K. Manh T. V. Gamzatov A. Tartakovsky D. M. Yu S.-C. Yang D.-S. Kim D.-H. 《Physics of the Solid State》2020,62(5):845-850
Physics of the Solid State - Structural and magnetic properties of Sr-doped Pr0.7Ba0.3MnO3 polycrystallines prepared by solid state reaction are presented. Samples were in monoclinic structure... 相似文献
100.
Hue Thi Buu Bui Phuong Hong Nguyen Quan Minh Pham Hoa Phuong Tran De Quang Tran Hosun Jung Quang Vinh Hong Quoc Cuong Nguyen Quy Phu Nguyen Hieu Trong Le Su-Geun Yang 《Molecules (Basel, Switzerland)》2022,27(7)
Epigenetic alterations found in all human cancers are promising targets for anticancer therapy. In this sense, histone deacetylase inhibitors (HDACIs) are interesting anticancer agents that play an important role in the epigenetic regulation of cancer cells. Here, we report 15 novel hydroxamic acid-based histone deacetylase inhibitors with quinazolinone core structures. Five compounds exhibited antiproliferative activity with IC50 values of 3.4–37.8 µM. Compound 8 with a 2-mercaptoquinazolinone cap moiety displayed the highest antiproliferative efficacy against MCF-7 cells. For the HDAC6 target selectivity study, compound 8 displayed an IC50 value of 2.3 µM, which is 29.3 times higher than those of HDAC3, HDAC4, HDAC8, and HDAC11. Western blot assay proved that compound 8 strongly inhibited tubulin acetylation, a substrate of HDAC6. Compound 8 also displayed stronger inhibition activity against HDAC11 than the control drug Belinostat. The inhibitory mechanism of action of compound 8 on HDAC enzymes was then explored using molecular docking study. The data revealed a high binding affinity (−7.92 kcal/mol) of compound 8 toward HDAC6. In addition, dock pose analysis also proved that compound 8 might serve as a potent inhibitor of HDAC11. 相似文献